Perhaps.
It could also be the case that the reason the planet fell apart was that the torpedo was detonated inside a nebula, and didn't have a complete planetary surface to work on.
True, Saavik did say that protomatter was dangerously unpredictable, but this is not proof that protomatter was the reason for the downfall of the Genesis planet. It could have been the other thing.
Besides, the Genesis cave didn't show any instability, did it? That time, the process worked exactly as planned. Not so for the planet.
It could've been a variety of factors (since the cave was a controlled experiment and everything about the Genesis planet's creation was by chance. But, no one, including inventor David Marcus, suggest that the planet is doomed because it was made out of a nebula. Also, if Genesis worked, it would still be used in the future. That suggests that Genesis was flawed from the beginning, and the protomatter is the reason why (the cave could've had a longer shelf life then the planet by being smaller, programmed correctly, or some combination). At any rate, all materials I've found related to the movie back up this explanation.