.
To resume both choices don't really change much.
If you spare Jake he appears a couple of times, gets captured by HERO and joins as a conscript, helps Mc fixing Mia's memories and she is VERY upset with him but he has some closure on the subject.
If you kill him he is safely stored inside you like everyone you absorb, so no relevant interactions, you also fix Mia by yourself.
It is implied before that Mia won't forgive Mc if he kills Jake so this might become a consequence eventually, also he features in a dream in both cases, where he helps you and you can help him too or just leave him trapped, there is also no advantage in stats or any new powers if you kill him.
Personally i think is more of a story choice for now, but maybe with version 1.0 a few things might change from early game.