Karma is used, but only in so minor places, it's not worth to mention. What we use - and what the op wrote about - is reputation
What I can say is, that the BoS will never open the fire in encounters, if you aren't their enemy. With the Enclave, it will change again in future.
If you want to make enemies, try to change something.
Karma is used, but only in so minor places, it's not worth to mention.