I understand your point and it's a very valid concern. Someone will please correct me if I'm wrong, but I do not believe you get negative rep with the faction you are fighting against in the combat zone. I'm currently Allied with the Feds from trading, missions, etc., but fighting for the CSG in the combat zones and the Spear of Lugh mission. I haven't seen any negative effect to my standing with the Federation, and there are no red arrows when I turn in combat bonds. If more commanders knew this, they might be more likely to side with CSG for this conflict.So, if I fight for the Crimson I get...
+Money from combat bonds
+/-'Free' the system, and install new government
-Rep lost with the Feds
-Probably blown up by a capital ships.
If I fight for the Feds I get..
+Rep with the Feds (and their entire network of Fed controlled systems)
+Money from combat bonds
+Capital Ship support (which means more money)
+A community goal that I can actually do efficiently, and enjoy doing.
-Lose CSG rep.
So the choice is pretty easy for me.
Honestly, I think one of the problems here is that unless you are an avid reader of the forums, you really wouldn't know the effort that player commanders have put in to get the situation to this point. The casual player would just pick the side that's going to earn them the most money and combat rank. Right now that's siding with the Feds with a cap ship. I consider that very unfortunate for the players who have put in so much time, testing, and effort. If this was mentioned in the newsletter for instance, I think CSG would get much more support.