Related to this:
I took a Hegemony commission and went to Valhalla to track down some filthy Tri-Tach because Hegemony were openly hostile. I get to the system and get attacked by pirates. Because there are Tri-Tach bases in the system (and possibly offering a bounty), I gain 3 rep points with Tri-Tach that puts me into "Inhospitable" rather than "hostile." A few days later, I'm hit with a -5 rep to Hegemony because I'm not hostile with Tri-Tach.
I get that I'm supposed to be hostile toward the faction but as in the case above, not attacking the pirates because of a rival factions bounty (and subsequent rep improvement) doesn't make sense. I still get commission payments for killing pirates so I still want to attack them. As the OP suggests, if I accidentally move from "hostile" to "inhospitable" against a rival faction, I may have no recourse immediately and suffer a rep hit for doing my job. I know this wouldn't solve all the problems but in my particular case, dropping my rep to -55 (from -50) when I took the commission would keep me from going to "inhospitable" for the smallest favor to a rival faction.
Alternatively, if you accept a commission, perhaps -negative reputation with rival factions increases a little every few weeks or so (up to a set max of say, -60) just because rival factions hate your allegiance. I don't want a hole I can never dig myself out of but if I accept a commission, I understand what I'm getting into. I don't think having long-standing commissions should automatically boost your faction rep with the friendly faction but it would stand to reason that rival factions grow increasingly frustrated with you the longer you're allied with a given faction.