I think the vast majority of physicists have been perfectly able to avoid Penrose's error. I would also think the lesson would be simply to strive to avoid making errors or the kind he did, not necessarily to sacrifice realism about physical objects just to avoid the possibility of someone's mistake. Plenty of people, in fact I would say many more people abuse the observer effect in QM to make crackpot claims about consciousness. But it doesn't mean the observer effect is wrong.

I also think you can be a realist without having to make the jump to ontological irreducibility. You can say that our latest theory is a better approximation than the previous one and the previous one was an approximation as well.