Okay to explain this, I basically entered the Silver Rush shop and when I tried talking to one of the guards I somehow made them hostile and they attacked me and it came up with Birds of a Feather Failed?

Would it still be possible to do said quest if I leave them alone for a couple of days (like in FO3), I didn't kill anyone and merely just ran away though Boone technically killed two outside the entrance but I heard that may not count as Player interaction

Don't try to walk past the guards until the conversation in the shop is over.
If you don't have a recent savegame to revert to you are probably out of luck.