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So:

In Spiderman 2 it's pretty clear he has two-way communication with the actuators; they aren't screaming at him to do their bidding or taking matters into their own hands, like the Green Goblin did with Norman- they've gone through the effort of making sure their creator (or "father", as they refer to him in the novelization) is on their side. They care about him!

They:

Shield him from danger/harm on several occasions

Perform small, unrewarding tasks for him (lighting his cigar, holding Harry's glass of liquor to his mouth, taking off his hat in the bank)

Treat him delicately, as is shown when they gently remove his blindfold and wait for him to wake up in the hospital

Don't use any physical violence or restraint whatsoever to maintain control over him

When he's out on the dock and mentions needing money to rebuild his machine, only to reassure himself that he's not a criminal, it's shown that the actuators begin talking back and forth with him, convincing him that such a crime would be justified as implied by Doc's dialogue ("You're right, the real crime would be not finishing what we started"). He then colloquially starts referring to him and the actuators as "we", completely by his own volition. He's being influenced by them, but not brainwashed- if he was, then there's no way he would've listened to what Peter had to say during the final confrontation.

My point here is: the way that Doc is controlled by his arms probably doesn't seem like control to him. If the novelization (once again) has any say in it, he sees them as his offspring ("My babies are multi-talented") and likely trusts and cares for them just as much as they do for him. Their control of him relies on the manipulation of that trust.

So, when MCU Peter decides to replace his chip against his will, I can't help but think that the dead silence he heard upon waking up/rebooting must've been absolutely devastating.

It doesn't make sense to me that he'd feel nothing but immediate relief and gratitude, as from his point of view, Peter essentially just murdered his creations by removing their individuality and reverting them back into mechanical puppets. Even if it did come as a relief of sorts to him, I'm inclined to believe he'd also feel empty, lonely, sad, grievous etc- a parent would be grateful that their child stopped crying/throwing a fit, but not so grateful if they discovered that their child was dead.

Similarly, somebody might be grateful in the long run to have escaped an abusive/codependent relationship, but still go through immense pain while coping with the loss of it- especially since psychological/emotional abuse often relies on gestures of love and positive reinforcement to keep the victim from leaving.