I doubt you'd have any real issues as long as you're not making any profit (directly or indirectly), it'd be no different to people using WoW models in sc2 and as far as I know Blizzard haven't said they mind people doing that.
HOWEVER... I think you'll find yourself having a VERY hard time getting War3 models to work in starcraft II, its not simply a matter of running them through a converter, the games work in very different ways and even should you succeed the war3 models being all low poly and texture quality would look just awful next to sc2 doodads and terrain.