Aw, Genesis as detonated in the movie shouldn't have worked at all.
What was it Carol Marcus said... "There can't be so much as a microbe or the show's off."
Well it's pretty certain that aboard the Reliant, there were microbes. Even if Khan and every person aboard was dead at the time of detonation, it'd only been minutes since their deaths. Lots of bacteria and microbes and undead cells and whatnot still in their guts and stuff.
That alone could have explained the later problems with Genesis, without the need for inventing protomatter.