1) The Disengagement Rule is needed. Now remember, I was an Air Force guy, so I know a lot about the whole fight or flight thing. If I am in my fighter over, say Iraq, and someone fires a SAM at me, there is no magical red safety line that I can just go run over and not have to worry about the SAM anymore. Infact, if I am over someone elses territory, and get caught, the US, though they will care about it, and hope that I can make it out, won't be able to do anything about it, and I have to fight for every mile that I get closer to friendly air space. It shouldn't be any different here, if I find someone in the middle of Fed space with a bumper sticker on his ship that says "Earth or Bust" there is no way in hell that I am going to be happy if he gets to run over a little red line and be safe again.
2) Line of Supply is something that is needed, but it should probably be more of an Area of Operation than a Line of Supply. Again I will use fighter jets as an example. You can only put so much fuel on a jet, so it can only go so far, but there are no real boundaries as to how far in which direction, it can go a certan distance in one big circle before having to turn around for a refueling. Back a couple years ago, when I waas still an Admin for the SFC3.net server with Mike Day, we tried a system where the bases provided a certain range of operations, and a planet an even larger area, no matter what color the hexes around them were. The only stiuplation was, that to provide the area of operation, the base had to somehow have a connection to your homeworld. It couldn't be placed off 30 hexes into nuetral space in the lone hex your race had manage to capture. This seems like the best option to me, but again, that is just coming from an Air Force guy, I really haven't ever dealt with the concept of boundaries on land and in air. You either have more road to drive on, or you don't simple as that.
3) Nothing else comes to mind at the time, but give me time, I'm sure I can come up with something else.