When Simon arrives on the Hail Mary he brings a shit-ton of blood with him. Grace of course tries his best to clean it all up, but his first priority had been getting Simon to Armando for medical attention, and by the time he comes back to deal with it, some of the blood has seeped into the body of the ship where he can't reach it.
The blood is alive. It infects, mutates, and fundamentally changes whatever it comes into contact with, which includes the Hail Mary.
Shortly after Simon's arrival, the Hail Mary is alive too.
However, the key thing is this. The blood ocean was a malignant entity that thought it was helping humanity by absorbing them. The Hail Mary is genuinely helping humanity to find a solution for the astrophage crisis. Her purpose is to save humanity, to keep the humans aboard safe and alive so that they can fix the problem. So when she comes to life, that intent is going to carry over. Suddenly she has the capability, the capacity, and the desire to keep her crew safe.
Mary may be alive now, may be an honest to goodness artificial intelligence now. But unlike the blood ocean, she genuinely wants to do what's best for her passengers, which now include a rock spider and a very fucked up mutated human from another universe.
Just picture a sapient Hail Mary trying to do whatever she can to keep her new crew alive. Something breaks in the lab and starts emitting toxic fumes everywhere? She locks down the room until it can be safely vented. Unexpected asteroid in their path and no one is close enough to the controls to navigate them out of the way in time? She just does it herself. The more time passes, the more control she has over every part of her structure, to the point that maybe she's even able to repair parts of herself like a living thing heals from wounds so that Grace has less to worry about.
The cosmic horror leaked into the Hail Mary, but she just turns it into cosmic hope again.
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