Doesn't everyone imagine themselves to be one of the 'good guys'? Surely the 'bad guys' in your example will also be telling themselves they just have to do some bad things to defeat a truly bad foe.

Does it even make sense to speak of 'good guys' who do bad things? Intentions count, but at some point I don't find it unreasonable to call someone who is doing very bad stuff a bad person, no matter how they rationalize it to themselves.

Which ethical theory are we using, anyway? Sounds like consequentialism is assumed?