I came into this a tad late, but here are my two creds about faction/indy relations.
Factions have layed down a lot of the groundwork for the current diplomatic state of Disco. Indeed some (TBH amounst others) share their diplomacy with the entirty of the faction. In cases like this (which is widely accpeted as ok) I think the player faction has the right to lay down the law with the faction as a whole. The roleplay of factions does trump indie's roleplay as it involves more people. Now like it or not, a group is more inportant than a lone individual.
However I do believe that factions (especialy the 101st Eppy if you read this) need to comunicate what they're doing better and more calmly with the people who are willing to listen. Respecting the roleplay of an Indy is very very important. Most of the truely innovative rolpelay comes from indies, as they're not so constrained by faction politics. Factions should listen carefully to the indies and try to find a way to accomodate them provided their roleplay isn't utterly absurd... "I am a ninja pirate cyborg, with psyhic powers that flies a battleship on my own cos I bought it lolz" isn't going to wash with anyone, and factions are right to stop this kind of behaviour. However what factions shouldn't do is stop the slightly unorthodox RP that sometimes crops up. So long as it doesn't piss all over the established status of the faction as a whole then it should be seriously considered. Perhaps adding suggestions if it doesn't suit, rather than just saying "NO!".
If we all had a touch more understanding and respect for each other's roleplay rather than focusing, blinkered if you will, on one's own goals, then we would have far more constuctive communication between factions and indies.
In short...
Factions can, do and should weild a certain amount of power over certain things indies do (cap-ship purchase for instance), however they should respect individual roleplay and only outright refuse stuff that is obviously stupid, and in all cases communicate more, and give suggestions as to how to imporve the story to make it fit better with existing canon.
Indies should respect the fact that the official factions are the primary authority for the faction they roleplay as. Ask them before doing anything which could potentialy damage the factions (or another indie's) roleplay. I believe that indies should also inform (at least) a faction if they intend to buy a capship, and state what they're going to be using it for. That way we at least have some prior warning before the fleet of OC 'LOL' dessies decend upon manhatten, and can (with any luck) avoid it all together.
Angry communication would be avoided this way except when people refused to listen. Compromise is the key on this from BOTH sides.
None of this should be placed in the rules, however maybe we could have somewhere that all the faction specific rules are easily on display.
Another issue here is wether or not breaking a faction specific rule os sanctionable. I think not, however geniune respect for one another should come way before the rules anyway if we all had respect for each others roleplay then I'm sure there would be less sanctions anyway.
EDIT: N00bl3t, I have just read the RP for your Dessie again, and I quite like it It does in my opinion, need a few little minor adjustments however on the whole its quite good... I regard ANYONE who flies under Outcast colours as an Outcast, unless they are one of those 'ninja pirate cyborg from planet awesome in the awesome sector of the awesome pwnt you n00b galaxy' types. And then I don't regard them as being roleplayers, therefore not having a place on this server.