Sometimes when I read crazy ideas like these, I have to wonder if we're either on the precipice of something horrible - like two halves of plutonium banging together and going critical, or something great, like the birth of the internet. The main issue here is the risk taken in doing so. If your baby 'breaks' bitcoin (For whatever duration - either temporarily or permanently), will the usual sentiment I see from software engineers the world over - usually along the lines of "Well, if 'X' couldn't handle it, then 'X' is stupid and deserved to die." - going to be enough to placate the angry mob of now-bereft bitcoiners?
Of course, the flip side is supposed to be "well, if we didn't do new things no progress would be made" -- but I've yet to see anyone say "Lets test this idea out responsibly just in case we totally fuck something up." It's all SHOVE it into the live production network and see what chaos it causes - "Oopsie!, we're just trying new and crazy ideas guys, so sorry for screwing over the rest of the community."
There has to be a better way than working on the jet engine while at 30,000 feet in the air - just saying.
MasterCoin won't cause problems if it doesn't work, because it will never get big enough to cause problems.
If it does explode, then yes, it is likely to cause more "growing pains". If it causes plutonium-going-critical level of problems, then either bitcoin wasn't truly scalable, or bitcoin will recover. I don't think most people would just give up on bitcoin because of growing pains though, even extreme growing pains, as long as there are technical solutions to deal with them.