In Skirmish mode a stalemate seems to exist if no one has attacked or capture a building in quite a while. You get a 1 minute warning to quit stalling or else a stalemate will occur.
Taking enemy bases is certainly quite difficult, but there are options. The Shaman has skills that can lower damage you take and remove enemy units from the equation, the Warlock has skills that can remove single enemy units and bomb static defenses, there are Kamikaze troopers, and of course there are Devastators with siege mode.
Imagine a PvP game that had been very back and forth the whole way through, and the population pool has run out, both players own 10 Armours and 6 Anti-Ground Turrets. This is a no win situation for either player, whoever makes the attack will lose the game because the other player will have the assistance of turrets.
That's a highly unikely scenario. Yes, it is possible, but if you screw up your planning so much that you're stuck with 0 money at the end, that's kinda your own fault.
If this scenario is a Skirmish game, both players can sit and do nothing and get a stalemate.
If it's a campaign game, then both sides losses will be high enough that pretty much no one will have any survivors worth noting on the Strategy map anyway. Yes, you might lose a country for a turn, but the enemy will have lost most of his attacking forces as well.
If both sides have 200 recruits left, then those who spends them best will win. In Skirmish, Devastators will help, in Campaign, your researched abilities will help.
I don't see how this amazingly unlikely scenario of exactly equal stuff and money needs to be addressed by the game more than it already is.
Again: In Skirmish, there is a stalemate timer which will kick in.
In Campaign, if both sides have drained the map and their coffers dry, the winning side will get maybe 1 unit back on the strategy map at best.