Sort of negates their responsibility for their own actions, doesn't it? Didn't you yourself once argue that just because The Enclave was started and run by thoroughly rotten men using despicable means to achieve questionable goals didn't mean that it was fair to write off the driving philosophy underlying it all or to condemn their rank-and-file? I think The Brotherhood deserve the same consideration.
The things the Brotherhood "teaches and enforces in its children" are just as capable of creating Veronicas and Sophias (FO1) as they are of breeding fanatics like the ones that mow down the Followers outpost, and that dichotomy between hawks and doves (or at least hawks and more contemplative hawks) has been a defining feature of The Brotherhood since the first game. As a matter of fact, your conversation with your attackers outside the bunker, if Veronica decides to stay and you try to present her as benign, seems to very clearly indicate that the actions they're taking are well beyond the bounds of what's allowed by the Codex-- really, they're acting against the Brotherhood's law and teachings because of their own twisted interpretation of them.