Sorry for the late response! Itch needs a better notification system. ^^'
But to answer your point, that's okay! I want decisions to feel like they matter, so you'll probably encounter this a lot. :P
If it helps you decide, the weekly materials aren't fully implemented yet. Eventually there will be a small chance at a rare item if you go that route. Finn will also be a difficult character to gain friendship with, and going that route will expedite the process at a cost of said item.
As for the enemies, if you like them, go for it! At the moment there aren't many perks for raising their rep, but there will be later. The only benefit right now is with the outlaws. If you roll the mugging scene in Mardoc, they won't steal from you. There will be other things like that in future updates for all enemies.
The next update also heavily focuses on the outlaws and there will be a lot of ways to influence reputation with them. I wouldn't sweat grinding out reps unless you really want to.