Sorry but if I'm a Sith and I have the chance to stab a Jedi in the back Ill do it. the lore works that way it dose not work in anyway to where they work together for anything.
Try to look at it this way.
Big super badass monster shows up its going to destroy everything. Sith Leader lies to jedi and says ya we will work together but while the jedi starts to fight said monster. Sith "dose super awesome thing" kills both the jedi and the Monster in one blow.
Because this is a MMORPG it can't work that way cause one side would have to lose and they would get pissed.
And if they did a Your side won other lost thing both would be annoyed due to it not making any sense with the rest of the lore in the game and at the same time would end the game.
Now this is something EA/BW won't do they will just do like you said make a work together until said thing is dead and its lame as hell that way.
Not to go off topic but as I said things like that work in WOW or other mmo's but in Starwar's its a no.