before you do anything silly, keep in mind that will only apply when in dawnstar hold. in whiterun, it won't have any effect.

Marked her for death....

if you ran from vilkas, you can still join, even if you killed him(though i think he is essential), i killed four members of the companions before joining, brill, the maid woman(forgot name), torvar, and athis, the guards ignored the fight even after it moved to the whiterun stables, so i assaulted a guard, yielded, then i went back to jorrvaskarr and talked to kodlak about joining, now, i am the harbinger

I've only read the first post and I can tell you that Farks and Vilkas are assigned to the Guard Faction so that's why they act like guards of the city.

Farkas also has proficiency in blacksmithing and other non-warrior perks that make him a bit bugged like sneaking when you're not and stuff...

I'm on the 360 and I have the same problem. I even served time in jail to try to clear it, the guards leave me alone but Vilkas constantly follows me around. He converses with me with sword drawn. He will not attack, but I just can't get away from him. I've run far from Whiterun and he will follow me. I only ran a couple of the Companion quests. The only way to get away from him is to "defeat him," and as soon as he hits the ground fast travel somewhere else. It's very inconvenient since I do almost all of my business with vendors in Whiterun.