From a GPU point of view I suspect it would probably just be a --kernel option
(and the kernels would have to have extra info about verifying shares)
The extra scrypt GPU options may or may not be necessary - I'm sure he'd work that out.
Of course, as the README already says, and has said for a very long time, you wouldn't be able to mine 2 different coins in one cgminer instance.
The current reaper cl file will do >400KH/s on a 6950 mining solo using the linux code
I tried that a few weeks ago when that represented 6 blocks a day - I got 3 blocks in ~12 hours
Now I guess that would be 1 or 2 blocks a day.
When I tried that on a pool it dropped to a bit over 220KH/s
So yes the linux reaper code dealing with talking to a pool is ... well ... crap

The side effect of adding scrypt to cgminer GPU mining will certainly be to make CPU mining even more pointless on LTC.