Dont judge a entire faction on a few idiots. Thats like judging the legion on lanius, or judging NCR with colonel moore. I can guarantee the brotherhood elder didnt send those men into the followers camp to kill the doctors
You can judge the Legion by its violent aggression, just like you can judge the BoS by its dogmatism, xenophobia, and short-sightedness (which Veronica mentions, and is 100% correct about). While the BoS might not want to torture, enslave, or kill you just for funsies, they'd have no qualms with stealing any high end, pre-war technology you owned, before leaving you to the mercy of the wastes.
The non-renegade BoS in Fallout 3 (ie, Outcasts), were quite callous to the plight of people outside of their order; something they share with the New Vegas branch. If you're not a member of the BoS, can't/won't directly help them, and don't posses any high tech equipment, then you're - at best - worthless in their eyes. If you
do possess high tech equipment, they'll be looking to rob and/or kill you for it. Not exactly "good guys" as a whole, even if a
few of them aren't nearly as dogmatic as their rules command them to be.
And whether the "few idiots" that murdered the Follower of the Apocalypse doctors were sent by the elder or not is largely irrelevant; they were, in fact, adhering to the Brotherhood's rules in committing their crime. They suspected that Veronica had shared knowledge with the Followers, so therefore they (and you, and Veronica) must be killed. The current "decent" Elder in the NV faction is a human being, and he's eventually going to die off (unless of course he thought he could raze NV to the ground and steal Mr. House's tech). What happens when he passes on? Does that BoS faction get another "nice guy" in charge? Or do they get the run-of-the-mill dogmatist that cares nothing for stepping on anyone weaker than the Brotherhood in order to collect more technology; even if doing so means that the person(s) they stepped on end up eaten by death claws, radscorpions, etc...?
The BoS isn't exactly what I'd call "evil" - but they're not "good guys" either.