Well, as far as I can judge, you do take a reputation hit for attacking a faction even if you´re neutral with it (i.e. not allied, only trade rights, but maybe even attacking a faction you´ve got trade rights with carries a more severe penalty than attacking just a neutral faction), but this goes for "uncalled for aggression", i.e. an attack out of the blue. If, however, you assist an ally, you should be seen as trustworthy (especially if you actually agreed to assist your ally), however, whether the game mechanics share this point of view I have no clue.

As a matter of fact, even an attack after the diplomatic message "accept or we will attack" should increase your credibility - you´re a man of your word. Again, however, I doubt the game works this way.

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