Why would Ilya take away Berserker's reasoning? His madness ability does exactly that AND upgrades all his stats, but she only used it in the final fight with Saber.
Also why would she want to do that at all? Wouldn't a sentient Berserker fucking things up be even better? Worst case she could still use his skill.
So he can't betray her family and break the grail.
Then she could have just kept his madness ability on and giving him his power up
Uh I'm pretty sure she did. There is literally no advantage by doing so