I don't think it's that risky, if the WEC champ wins he moves up to UFC and defends his belt and they have a tournament to get a new WEC champ.
If the UFC champ wins everyone goes home happy.
The bigger dilemma I see is for guys like Brock Larson -- he lost in his WEC title shot so now what? The guy is easily good enough for the UFC but what do they do with him now?

I think a guy like Brock Larson, they can just throw right back into the mix. Put him against up and coming welterweights in the WEC. That's not a problem.

In terms of unification, we're atleast 2 years from that happening. The WEC is still building with the Wednesday show they're biggest one ever and I'm sure that trend will only continue. Filho, Faber, and Condit are all top ranked in their respective weight classes. Chase Beebe is a star in the making. Doug Marshall needs a few more dominating wins and he'll be a star. I think they just need to bring in consistent supporting role fighters who can compete with these guys and they're building a strong foundation.

I agree that it's more than two years in the future but it's a necessary goal for an expanding company--and sport--to make.  The UFC, along with all other promotions, can only support so many fighters in each weight class.  There will come a time when having 10 fighters in one weight class who could legitimately deserve a title shot will happen.  
This is where Zuffa controlling a second organization comes in.  Currently, the WEC is seen as a farming league, and for good reason.  But as it develops, along with the quality of fighters in the sport, the big brother-little brother relationship will slowly start to melt away into that of an equal or at least much closer match.  Having two organizations each with a competitive stable will create the polarizing fanbase that helped the recent mma boom that was lost in the Pride buyout.  As hated as fanboys are in any sport, their contribution to hype can't be denied.  And obviously Zuffa is not going to cross-promote with anyone else, so having the WEC is their only option to create these types of rivalries.