Like i said earlier, i think that Wario's incentive for helping the Subspace Army is money. He only cares about himself, and for a bit of money i'm sure he'd do anything.
However, the Subspace Army seem to be such a dangerous force that eventually they'll try to dispose of whoever helps them. After all, they are trying to swallow up the whole world into subspace.
With that in mind, i wouldn't be surprised (and would actually like) to see a turning point well into the story where Wario's promise of riches turns out to be a lie... or where he realises the seriousness of what the Subspace Army are doing and eventually helps out the good side. After all, if there's no world left to be greedy in, how can he be greedy at all? Maybe the same could happen with other playable villains in the game, such as Bowser.
It's happened with other enemies. Bowser has helped out Mario to defeat a greater evil, and Bowser is a bad guy, where as Wario is just a selfish self centered guy. Plus, in one of the Subspace Emissary updates Sakurai did say "People everywhere are moving against it," or something like that.
You never know!