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.
The specific part of the code that is crap is the logic for submitting shares. It stops a sharethread until it gets a response from the pool. To fix this you could
either rewrite the logic surrounding the threading (ie. just make a thread per piece of work when it is finished and leave it to itself) or you try increasing sharethreads.
Also try other pools, like ones that are close from a latency standpoint to you. But cgminer for litecoin would still be great.