A couple of things:
1. It's not necessary to root to get CWM on eMMC. See this thread:
When there's a stable autonooter for a given version of the stock OS, maybe it comes down to 6 of one, half a dozen of the other, but in many cases my method will cut out some steps, it works regardless of your stock OS version, and it gives you a test-drivable Gingerbread ROM in equal or fewer steps than rooting.
2. However, for most purposes you are better off running CWM from uSD rather than installing it to eMMC in the first place.