IowaMom - Through two sons, we heard all of that multiple times. Frankly, I don't think it really affected us other than make us think a little more, and maybe investigate. Actually, whether they were said or not, I asked plenty of experienced people about issues like the ones you mention about each school that was serious. And then we decided if it mattered or not.
Or...we even asked the criticized coach/program if it was true or not? Everyone critiqued Stanford for over-using pitchers - so I asked their head coach 1-on-1 about it. Then it was our choice to let it affect us, or not.
Everyone critiqued certain schools about running off players. So I asked each one of them if they would cut our son(s) if they didn't turn out to be good enough? Watching body language was more important than the verbal answer, by the way.
Many said, 'The coach at BlankSchool U. won't be staying long so don't go there.' So I asked all the coaches at BlankSchool U. if they would stay...or not? (Again, body language was telling).
I don't see a good reason to be afraid of such things. I'd just ignore it, investigate it...or ask about it.
College baseball is highly competitive (as you know) and once your son decides, it won't be the end of such comments about other schools/coaches (some are likely to come from your son) and about your son's own school/coach from teammates and parents. Not until he graduates will it die down.