My take on faction relations would be as follows:
1) If I have a high reputation with your enemy, you will gradually grow to hate me. Doesn't really matter what the source of my relationship increases was. If my actions have benefited your enemy you will not have a positive opinion of me.
2) If I have a high reputation with your rival, neither enemy nor ally, you will not wish to trust me fully. You have to wonder what are my intentions are in getting so buddy buddy with that rival faction? This situation could perhaps impose a limit to how high our relationship will go until my relationship with your rival has reduced to a particular point.
3) If I have high reputation with your ally, your trust in me will gradually increase up to a certain limit. After all, you are benefiting second hand from my actions. But since I'm not helping you directly there is a limit to your favor. Once again, you must wonder what are my intentions are in working with your ally and not with you. Until my relationship with your ally has reduced to a particular point you probably won't want to further our direct relationship.
4) Individuals are more easily influenced than nations. I've come to the aid of one of your commanders in the past and formed a positive understanding. This positive working relationship can probably exceed the limitations imposed above. This could be especially interesting in scenario 1, perhaps making me a double agent. (Friendly Tri-Tach officer asking me to install a communication sniffer in hegemony space in exchange for temporary access to station facilities and services.)
5) If I am caught actively acting against your interests, you will be vengeful. If I go pirating in your space and then try to improve our relationship in the future, you will make sure I have to prove myself worthy of trust. Or perhaps I may never be able to attain higher relationship levels until after performing a truly epic task to your benefit. Even then, you probably keep an eye on me and the trust degrades back down gradually.
6) Pirate hunting can only take you so far. Being a renowned pirate hunter probably opens a number of doors. But it shouldn't, by itself, be an invitation to your inner circle. Until I take the next step in solidifying our relationship you will likely limit my maximum relationship value.
So those are my initial insomnia generated thoughts. Please be sure to voice your own opinions as well.