You can alter Factions so that they'll offer Missions even if your Rep stinks with them:
Look at these lines in mbases.ini... here's where you'll want to edit things, for a Faction represented at a particular Base.
mission_type = DestroyMission, 0.000000, 0.112387, 100
The 0.000000 is the Rep Level that you have to have before they'll offer Missions, I believe (haven't hacked that for my mod, so somebody correct me if I'm wrong here).
Set it to -1... for every Faction that can offer Missions at a given Base.. and they'll offer Missions to you, even if they'd rather just stab you in the back
Note: I haven't done this myself, but I am pretty sure that's what and where you edit this. If you wanna do this for every location this Faction shows up in the game... that's going to take a lot of editing. Mbases.ini is probably the most convoluted area of FL modding