I believe that if you don't take missions but just enter the battle zone and collect the bounties and have them payed in at the station that then you don't loose any reputation.
I fought for Durius and I was alied with the Empire before. And I am still alied with them despite I killed many of their ships int his zones.
A related question:
As I remember, despite taking a combat-mission from side A in a war, you may choose side B when arriving at the conflict zone, shooting at ships associated with side A and, after having fulfilled your mission target, cash in the revenue from side A?
IIRC, the ware-zone missions
only ask for "killing kombat ships" and
never specify the side you have to choose.
Am I correct? And if I am... does this make any sense?