David was young and reckless in using illegal material to make his bomb, presumably because he loved him Mum and wanted her life's work to be a success. But she must have known what was going on too. Maybe he was covering for her when he confessed to Saavik?
Let's think about this a bit. David probably didn't hide a canister of protomatter aboard the Genesis torpedo as such - it's more likely that he programmed the Genesis process in such a fashion that at some point, creation and expenditure of protomatter was involved. That's something a software specialist could easily hide from a non-specialist. Well, not trivially easily, but still.
The question then goes, was David the team's programming specialist? He was the only one talking about cramming bytes into the thing. It's possible the rest of the team were specialists in other fields, while David was both the ultimate programmer with the highest clearances after Carol, and somebody who knew the most about the big picture after Carol. Or, for all we know, David was the brains behind the outfit, and Carol was the established researcher whose name brought the credibility and the funding.
Protomatter could in theory have been David's very own personal secret, then. Or then it was shared with Carol, or with the entire team, or with a thousand people in Starfleet. But how dirty a secret was
it in the end?
Saavik says the planet is not what David intended. Either she has read the specs (since she's supposed to be a mission co-specialist on Genesis), or then she simply reads David; it's a no-brainer in either case. David says that yes, the planet is a disappointment. Saavik asks why. David then says "protomatter".
David most probably is saying that Genesis failed because protomatter failed to do what it was supposed to achieve. Saavik chides him for having used an unstable substance or phenomenon that is known to pose ethical problems. But we get no idea what those ethical problems might be. So "ethical scientists" say the stuff is dangerously unpredictable. What does this matter? Does the stuff kill people or what?
Saavik subsequently accuses David of being responsible for the deaths relating to the Genesis project. But this is inane - those deaths would all have taken place even if David had not used protomatter, or hadn't been involved in the project at all. Every death was the result of the project existing
, not a result of the project being a success or a failure. So Saavik can be discounted as a reliable source for evaluating the worth of protomatter in the project outright - she's simply off her rocker. (Perhaps David is driving her insane with lust?)
So what "malpractice" would be involved in Genesis? Protomatter didn't kill anybody. Carol or David didn't kill anybody. Khan killed a lot of people, and Kirk then killed some more, but that's got nothing to do with the Marcuses or their scientific work.