You have been listening to Larry too much!
At this point, as we are still in the testing stages of the project, I do not see the lack of normalization as a problem. After the current protein we will begin much larger runs on much larger proteins. I am assuming that the trend will be towards larger and larger proteins (not a direct increase at all times, but a general trend towards larger protein sizes). So, the lure of waiting for a 'fast' protein might very well be suicidal rather than 'cunning.' With more of the major teams getting involved with DF, I don't think that further down the road, a single team (however large) will be able to sit out month long runs and then pick up the slack by allocating massive amounts of boxen on the project for the next protein. Ars, DPC, HardOCP, DSLR they might all be able to swing a couple hundred GHZ for the span of a month, but if a protein is THAT small, the other teams would most likely be doing the same thing, thus "normalizing" the stats in a somewhat "natural" way.
Until it proves to be a barrier to further growth of the project, I think the varying structure computation times of different proteins is not something worth worrying about or investing a lot of effort into.
SETI doesn't normalize for different angle ranges, do they? A WU is a WU and over time it 'smooths' out.