Maybe Raphael was telling the actual truth when he said that he could become a friend. Mindflayers are of no worth to him. If we help him to stop them that means more potential recruits for him to make deals with.
Priestess Gut is not exactly the brightest light on the absolutes chandelier.
Out of game spoiler:

Some mindflayers want to create a group of super soldiers. True Souls. They seem to cooperate with the entity behind all of this

I sometimes use thought experiments. I don't necessarily believe in every idea I post for discussion on this forum