I've had comebacks from a single planet situation before, and won.  I just got overwhelmed by the 4 other Vicious opponents in the same system as me.  To me, this just seems like the game saying "I win because I say so!"  Other games have similar victory conditions to the one I'm suggesting, where you have a certain ammount of time to get a building back on the map.  2-5 minutes is a perfectly reasonable ammount of time.  I could have had the 4 planets in that system completely locked down, with Starbases on the star, and came back stronger than ever.
Mostly, I admit, this defeat was my own fault.  I wasn't paying attention to the phase lanes and got backed into a corner with no way to escape.  I should have done what I always do and abandoned the Home system Immediately to lock down a neutral, but I was playing around with the Diplomacy tree and got steamrolled by a 4 Cap-ship advent fleet, with support, when I only had a Kol and 8 Cobalts and a single Roid. 
Still, the game ending when you still have a way o expand is ridiculous.
Alternatively, how about having your ships take damage over time when you own no planets, as a way to show they are cut off from supplies, and have the Victory Conditions be met upon destruction of the last Colony frig/Cap you have.  Compared to other suggestion's I'd offer, this would be very reasonable.
But don't take anything I'm saying too seriously, I suppose I'm just mad that I lost when I was so close to getting back in the game.
-Exile Ascendant