Not really. It's more like this. You are a good person, but you had this really evil asshole come and kill your friend right before your eyes. You chase him and he runs past this cop. You either do or don't see the cop, that's not important. What is important is that when you catch up to the guy and try to kill him, this cop sees you.

Now the cop is also a really good guy, but he didn't see the evil asshole kill your friend so he is going to do what any good cop and good person would when they see someone trying to kill another person with no context. Stop them. So he runs at you and when you don't lay down right away he tries to make you go down. So he attacks you and you kill the cop, who was also good. Now, that doesn't mean that you aren't good anymore. But the choice you made was not a goodly choice.

You can justify that you were defending yourself, and it's true that you were, but that doesn't make killing this good guy cop a good route to take if you care about being a good person.

In CF the laws of the Tribunal cities require blood if broken, so the guards aren't going to arrest you they are going to try to exact that price. It's something all goody Tribs try to avoid, but if it comes down to letting you kill someone in the city while they watch or their duty they'll likely engage you. And if you don't run away from them then they will fight you to the death. Now as you that's fine if /you/ stand there and kill them because it would literally be self defense, but if you belong to an organization with principles and guidelines like Fort then you are expected to retreat and do everything you can to avoid shedding that good guy blood. Even if that means you go run yourself on to a big bad mob to lose the flag.

Cityguards aren't out of their minds and just attacking you for the psychotic lulz, as well, so even though those kills are in self defense you shouldn't make it out like they attacked you for no reason. Get the (Criminal) flag and they are all going to attack you, it's not a surprise party.

Edit: It just occurred to me that if you make another character you should roll with an evil. Problem solved, you don't have to adjust your mechanical play to compensate for your roleplay, kill or don't kill whatever you want to. In Fortress, you are expected to divorce yourself from available mechanics in favor of RP driven responses.