At least take away a core and find a way for him to live short life like a normal human. from what I understood, that is what he want's. Freedom to live how he wants.
I will be seriously disappointing if they decide that all those 5000 years are nothing, all suffering doesn't matter because of few weeks with random people.
@BananowyJE What Shutina will probably say will answer your comment. AS she said there's a huge contradiction in Leo's story. If Leo has managed to evolve and surpass some of the restraints placed in him. Then it's quite possible that he has evolved beyond his programming. Meaning, "Protect Humanity" may no longer affect him. Like at all.
MC has managed to start plans against humanity to protect, this don't just show that he gained the ability to interpret his orders in a different way, he should also have earned the ability to completely ignore it. What happened is that he is now being limited by fear of what he thinks he can do if he keeps following his order, never noticing that his orders should no longer affect him.