If You Don't Understand why Alex Wasn't Punished for the Prank, you Haven't been Paying Attention.
There's a difference between understanding why Alex wasn't punished for the paint-and-feathers prank and believing that she deserved to be punished for it. I totally understand why fans would be upset that she didn't get the same treatment as Spinner and Jay seeing that she actively played a role in Rick's humiliation, which led him to...well, you know. However, there is a sequence of events that play out in the episodes after the shooting leading up to "Eye of the Tiger" (4x16) that explain why the events played out as such.
"Do you wake up every morning thinking you can walk and then remembering that you will never, ever, walk again?! It's not your fault...it's mine." --Jimmy Brooks, "Eye of the Tiger"
We get glimpses of Spinner in "Back in Black" (4x09), moments where he doesn't say anything, but is communicating through his facial expressions. It is evident that Spinner is riddled with guilt after he and Jay lied to Rick in the restroom, telling the kid that Jimmy was the mastermind behind the prank and set him up to be humiliated on stage in front of his peers. This is the event that drove Rick to retrieve his gun from his locker and shoot Jimmy in the back. Remember: once Rick was in the restroom cleaning off his face, he had decided to suspend his quest for revenge or at least prolong it before Spinner and Jay entered the men's room, causing Rick to hide in one of the stalls. Once Jay and Spinner identified Rick's paint covered dress shoes behind the stall, they proceeded to have a fake conversation and threw Jimmy, Spinner's friend, under the bus. After Jimmy had been shot, Spinner had been grappling with the guilt for months until he could take it no longer. The stresser that caused Spinner to break was Jimmy's return to school, confined to a wheelchair for what could be the rest of his days on earth. He tried to ignore it by overcompensating on Jimmy's behalf, constantly rushing to his aid whether or not Jimmy requested his help. Then, finally, Spinner and Jimmy are in the gymnasium alone, and they address the elephant in the room: Jimmy may never walk again. After Jimmy laments, he then blames himself for Rick coming after him:
"Look, stuck in a bed for three months, you can't stop thinking...about Rick, and how I rode him just as hard as you guys...even harder."
The icing on the cake: Jimmy confesses that he wishes Rick "had better aim", implying that he would have rather been killed than to live without the use of his limbs. "It's not your fault." Jimmy says to Spinner. "It's mine." He looks away from him, appearing frustrated, discouraged, and disappointed in himself.
It's at this point that Spinner couldn't handle hiding the truth from him any longer. He proceeds to tell Jimmy that he and Jay told Rick that Jimmy was behind the prank. Jimmy then connects the rest of the dots. "And then he shot me." He says. He pauses, then leaves Spinner alone in the gym. As a result of his confession, Spinner loses all of his friends except for Jay. This includes Paige, Hazel, Marco, Craig, and even Manny, who he had been dating briefly until that point. Spinner would later show up to their party drunk and beg Jimmy for his forgiveness, but Jimmy isn't having any of it, and he is brutally honest with Spinner on what he thinks about him:
"Why don't you for once just think of somebody other than Spinner? Or you know what? Just go drive off a bridge. I don't care, I don't. You're dead to me already."
Jimmy was heavy handed, but Spinner received the message loud and clear. They were no longer friends. That bad blood between them would last for more than a year.
Finally, we end the episode with Spinner's confession to Principal Hatzilakos, who had been newly appointed after Raditch had been reassigned to a different school. He admits to bullying Rick constantly and to being responsible for the Whack-Your-Brain prank. "It was my idea." He told her, bowing his head in shame.
After a very long pause, the principal asks, "Is there anyone else I need to talk to about that?" Her voice is calm and quiet.
Spinner gives away only one other name: Jay Hogart. Immediately Ms. H. calls for Jay to be pulled out of class and proceeds to expel them both, and that concludes the episode.
Have you noticed something here? I haven't brought up Alex once since the first paragraph. That's because Spinner's reason for confessing to the prank had little to do with the prank itself and everything to do with the staged conversation that took place between Spinner and Jay -- a conversation in which Alex did not participate. He was motivated to confess through his guilt of indirectly getting his friend shot: something that Alex was not apart of. In fact, very little of the narrative focuses on Alex at all, which is why I haven't brought her up until now. This story is about Spinner's redemption. Sure, Alex participated in the prank with Jay and Spinner; she set the whole thing up. It was Spinner, however, who additionally threw his alleged best friend under the bus. Jimmy wasn't a friend of Jays; he was a friend of Spinner's, so for him to participate in the lie to Rick that not only an innocent person was behind the prank, but his best friend at that, makes it that much worse for Spinner and only Spinner. He realized his mistake only after it was too late.
That isn't to say Alex wasn't feeling any guilt. If we look back at "Back in Black" (4x09), we can see Alex wanting to talk to counselors at school and begging for Jay to come with her. While Jay rejects such an idea, Alex tells him, "You may not need to talk about what happened, but I do." Jay relents, but not before warning his girlfriend to be careful about mentioning their role in the paint-and-feathers prank. Should Alex have been punished for it? Absolutely. However, she was not the narrative focus, and as I mentioned before, Alex wasn't the one who set up her own best friend.
There's also something else worth mentioning: after the shooting, the staff is not primarily concerned about finding out who was responsible for Rick's humiliation. It's not that it wasn't important to them that the students involved be punished accordingly; it just took a back seat to what was now the more eminent threat to the learning environment: gun violence. They are not actively seeking out the perpetrators of the prank but are rather looking for ways to stop gun violence in the future. They are trying to help their students, who are now considered survivors of the school shooting, some of them traumatized and devastated by what happened. The adults are stuck with trying to understand how Rick could feel so humiliated that he would be driven to potentially kill his classmates. That's a more pressing manner than to find and punish his bullies. After all, Rick would have been the main beneficiary of this justice, but since he is now dead because of the choices he made, and because he shot another of his classmates, the focus is now shifted towards how Degrassi can be made to feel like a safe environment for students again. The adults are looking for ways to support their scared students who still have to finish out the academic year after tragedy struck their halls. Spinner just made it convenient for the principal by coming forward, and he brought up only those who he felt played a hand in Jimmy's fate, which, to him, was only Jay and himself. In Spinner's mind, Alex had nothing to do with Jimmy getting shot, which was why he left her name out when he turned himself in to Ms. H. This was the reason why Alex didn't face any consequences. Spinner never gave her away.