To be cruelly honest, decide how you want to run things STARP. :\ this is one of those grey areas that really need DM adjudication. the other "answers" (even this one and my other one) are opinions, not rules per say.
Given that nobody can really tell you how to run things, you should ask yourself the following questions:
Do you prefer FranktheDM option: No, killing the good aligned person is evil, no matter the motivation/circumstance (the "thow shalt not kill" directive).
Or the wmaster's reply: various shades of grey allow it, it just depends on the motivation/circumstance. (the kill the infidell/unbeleiver or foe for standing against your mission)
Decide which you prefer, but make sure that the Paly playing player knows how you wish to run such things so that you are on the same page at least and they can make an informed appropriate decision*.
However given the Q, i'd say that you probably lean more towards wmaster's answer. And my view
Neither is wrong, just a style.
* Personal opinion here: it is one of the things that any PC Paly should have to face at least once in their life. Do you choose to kill or not to kill someone with similar views to yourself? It is also beholden apon the player and DM to have a workable view of how a paly should act, other wise it can degenerate into something neither person wants.