Is having a positive relationship with the mook important in the later game? I messed up and walked with the CM earlier and had to fight some..they had some pretty good stuff. I reloaded and did it right to keep my faction rating up with them, but if it's not a big deal in endgame, I'd kinda like some of their stuff...

No repercussions later in the game. As long as you have the CM, you are fine.

Granted, you will not be able to recruit the Mook in the house for your party, but no great loss.

No it is not that inporten but be friends with them to get both sides letter giving to them and get there`s stone!