He chose to help his mother develop the Genesis device, and he should have foreseen the potential the project had to go awry.
But the project did not "go awry", nor did its potential for such play a role in anything. The project merely existed, from which it followed that people got excited and murderous and protective and murderous and scared and murderous. What David did or failed to do did not affect that
Saavik further confuses the issue by suggesting that the use of "unethical" protomatter had something to do with it. That I think should be considered a totally separate issue. Perhaps use of protomatter kills kittens or something, and David thus should fry for that. But use of protomatter had nothing to do with the deaths that Saavik mentions.
n any event, she had the choice of developing Genesis, and David had the choice of helping her do it.
And that, I think, is the best way to summarize it: her choice mattered, his did not. Even if Genesis never got beyond wild white papers, it would sparkle excitement and could be connected to the deaths; but whether Genesis succeeded or not, whether Genesis got help from David or not, was not relevant to the deaths.
Regarding your scenario, kudos for thinking it up - might make for a good nuNovel, actually! But I don't really see the Federation hesitating from developing technologies simply out of fear of weaponization. After all, they are an interstellar empire: they necessarily engineer big. Anything
involved in such is by default an elephant, ideal for trampling in addition to its beneficial engineering uses.
Take something like "Homeward". It wouldn't take evil minds to devise a technique for stopping a disastrous dissipating of an atmosphere, but it would
take evil minds to stop the project just because it will also inevitably yield the means to do what the Klingons did in "The Chase": torching of a healthy atmosphere.
I still see no "blame" in the creation of Genesis. Creation of quadrotriticale was probably even more destructive for its conflict-sparkling potential and its use as a weapon, but it's also something that had to be done, for the same reasons that Carol gives in her marketing pitch. Starving millions for the off chance that somebody would get angry or murderous otherwise is not particularly ethical.