well, a third neutral party would create kingmakers which in my opinion (but i can of course be wrong) would be frustrating and unfair. why would you want to add some players that can decide of the winners?
For the two differents teams, it is definitely doable, but i am not sure of what it would add to the game.
I mean, if you kill one citadel, theirs allies are dead meat, so there is not really an interest in that option. But you could think of having two citadels for one team with a map shaped like that:
X X
\ /
\ / where X and Y are the different teams citadels
O
/ \
/ \
y y
And if one citadel is destroyed, the portals that are connected to it close. So it would still mean near immediate death if one citadel is destroyed, adding tacticals choices as where i focus my attacks and my defenses.