Your point is interesting, but what is star online then? Is it nothing more then a one faction game, with one faction pvp? I for one could not stand for something like that, it wouldn't be right star trek wise. Also there is not such thing as a Rebel Klingon house, to be a rebel Klingon house means to have no honor, that means no support from the Klingon Empire. Further more they would seek you out and kill you. Even the most powerful Klingon families that have been known to be disgraced end up with maybe one ship at the end. Those are only the most powerful. So you really could not say every Klingon in these matches escaped the clutch of the empire, and was able to procure a crew. That is a extreme stretch.
Excellent Post -- and you hit the nail squarly on the head. One faction PvP is not PvP at all, not really...yet that is what most of the Federation players are participating in. You have some extremely experienced Fed PvPers who are experts at fighting their own faction in these wargames...but who will not participate in Fed vs. KDF PvP at all.
Additionally, you inadvertently provide additional justification from a PvE standpoint for merging the two factions..because if the factions are merged, then the Klingons and Feds can go hunt down these "rebel houses" together....
For the record...if some sort of "merger" is in the works, I am completely against it as a player...not that this means anything in the great scheme of things...but if it happens, then I believe that it will be one more step towards "Star Fleet Online" rather than "Star Trek Online".