Some are fighting against the traitor Patreus rather than the empire.
I did some fighting at the CZ in protecting against Patreus and while it had no negative effect on my empire rank or me being friendly with them it also made me friendly with the alliance.
Easy way out for an mercenary, ey? "He isnt the true imperial, he is a traitor" and then you can fight against Imperial Navy? Dont make me laugh.
If PLC Electronics faction wins the civil war, the system will belong to the Empire. If Peoples Party of Judea... erm, i mean Quivira win, the system will be independent.
Every pilot fighting for independents is an mercenary at best. If you think of yourself as an imperial pilot and you still fight for the independents, face the truth.