This is one thing I feel the same. Commissions are a pain in the neck, since factions keep changing from truce to war FTL. In my vanilla game (no mods), I too got a Hegemony commission, until at least I got myself 3 of their largest ships and at a point i was caught smuggling by them and they disliked me and took away my commission. I was glad to get rid of the commission and not have the headache to run all around the map.
What I did to not make all the factions my enemies, to keep Hegemony happy, was to keep attacking 1 faction a lot and whatever points I lost from not being hostile with their enemies, I gained through attacking Tri-Tachyon, which was the faction they were at war the most.
For better or worse getting a commission means you are bound to attack their enemies and be part of their army in a way. FOr me After I got kicked out of their army, having 3 Onslaughts in my army from them, I did not care to be anymore part of them. Money in vanilla can come from trading. Having a fleet with 2 Atlas (6000 cargo) along with the cargo the rest of my fleet had, I could easily trade huge quantities of commodities and no one dared to attack me.
Afar from finding a way to survive in vanilla with how things work for now, I have a suggestion. If you want to experience a semi-vanilla game and enjoy Starsector's vanilla galaxy, you can use the Nexerelin mod and play in Corvus mode. You will play in the vanilla galaxy but with Nexerelin rules. That means factions will be able to invade planets and take them over, which will make the Starsector universe feel a bit more alive since you will see it slowly change. You can get commissions with them too, but in Nexerelin you are your own faction too. If you manage to raise a really big fleet, you can start taking over planets, with the easiest being the pirate ones. Your own faction will pay you a small amount of money monthly and will never tell you to run around all over the map to kill their enemies.
You get prisoners in the game, from killing enemy fleets. What can you do is for example; befriend a faction and get a commission from them. Buy the ships you want from them and ignore their request for you to attack their enemies. When they will dislike you to inhospitable level (-30 I think?) and take your commission away, fly to one of ther planets and use the option to repatriate prisoners. Each one you will repatriate will gain you 5 reputation with them. That means if you repatriate 6 of them, you will return back to 0 reputation and ignore them.. until you will decide to attack them to take over their planets and make them yours XD