I don't understand the issue here. It is normal that fighting against a faction is reducing your rep. And you don't need to redeem bonds anymore, just CZ completion.
What is the issue here ? Sorry, but I skipped the last pages.
Yes, you can still help win wars by means other than handing in bonds, but handing in bonds still counts. tl;dr It shouldn't.
Let me ask: Which faction should win?
The faction who has a high-intensity CZ cleared for them? Or the faction who has a high intensity CZ cleared for them, and pays 1m to some rando pilot for the work?
It should be a draw... because whether or not a faction has to pay out credits to anyone should have zero impact on the outcome of the war. Arguably, the faction who pays out should
actually lose, as they're more out of pocket, all other things being fair.
Specifically, for Phase 3 of the Interstellar Initative, by all accounts it's going to be your bog-average conflict CZ. These are won by whoever hands in the most bonds. If it's hosted in a station owned by one of the factions involved in the war, anyone supporting the opposing side will eventually be locked out of the station, and prevented from participating further, due to becoming hostile.
It's a game-breaker. Frankly, it doesn't matter if there's other methods you can do. The act of handing in bonds should not affect the outcome of a war, in terms of the BGS. It should depend purely on running missions, clearing CZs and finishing scenarios at USS.
And for the fourth time... nobody thinks you shouldn't become hostile for attacking a faction. But becoming hostile actively restricts your ability to undertake further hostilities. This is what's broken, and has been ever since FD made hostile-station-lockouts a thing.
Tangentially: The reality is FD have neglected antagonistic/aggressive/hostile gameplay for too long. This is easily proven with the current state of the galaxy, reflecting more of an Elite: Best Friends universe with the prevalence of Boom/Investment and Civil Liberty, and the near-complete absence of negative states. The
actual thing FD needs to do is invest in game mechanics which offer balanced rewards and equally incentivise pushing one faction into Investment and Civil Liberty, while crushing another into Famine and Lockdown. Somewhat cynically, this is never going to happen... but this particular issue is, like it or not, now a gamebreaker, and a product of that neglect. The easiest and most realistic fix right now is just removing the effect of combat bonds. Less-powerful commanders can still very easily contribute in low-intensity CZs, scenarios and missions, and combat bonds should nothing more than "a nice cash bonus".