You're going to commute on fancy carbon trispoke wheels? Please tell me you're not gonna be locking it up outside like that...
Here's my philosophy on commuter bikes though, so you know why I think using those wheels is a bade idea. If you have the option of locking up indoors in a controlled area, this is all null and void. I'm thinking only of areas where you'r locking up outside, locking up in public areas and where the bike will see a lot of day to day usage that doesn't always call for high end stuff.
IMHO, flashy paint, obviously high end components (like fancy carbon trispoke wheels,) big name brand stickers, etc, is thief bait. Highly priced lightweight components are things that will get beaten up on the bike rack by other people locking and unlocking their bikes. This is problematic sometimes for carbon fiber, since scratches and scoring, whether from punk teenagers of repetitive use of a bike lock, can weaken the fiber structure. And while wheels are generally built to be strong, carbon is carbon, and you want to keep it relatively safe from certain things if you want to use it for a long time.
I'm with Shiggy. There are too many good disc brakes out there that work very well, particularly avids. The "cheapest way to upgrade your braking performance" woudl be to simply replace the brakes you have. It'll be a lot easier to simply swap brakes, I'd think, than to go through the process of swapping everything from one frame to the other. ANd uless you're doing the work yourself, it'll save you a lot on labor, too.
If you're bound and determined to use at least one wheel, I suppose it's possible to switch the front to a V-brake, since I haven't seen too many disc only forks, and on the road, you should be using your front brake more anyway. But that just seems silly, somehow. It's a frankenstein half measure that doesn't really do justice to either the bike or the wheels.
Honestly, I think if you really want to use those wheels, I dont' blame you if they're that nice. I've had wheelsets that have collected dust while I tried to find a place for them, because they were too nice, and I didn't want to get rid of them. But forget them on this frame, and work first with the bike you have. If it's already a good commuter bike, buy some servicable disc brakes first. Then research what sorts of bikes those carbon wheels are normally used for, and build a bike around them. It'll be a lot of fun, you'll learn a lot in the process, and you won't suffer the same crushing heartbreak if you come outside and find that some nitwit has run over one of them while it was locked up by the roadside.