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My hypothesis is pitchers at low level D1's are much more likely to be abused than at the upper programs. I think this is a combination of coaching (better coaching at the higher levels) and at the lower D1 levels coaches want to get wins given the opportunity at all costs. Wins can be far and few between and they are looking to climb the ladder to better positions.
I need a lot more convincing on your hypothesis.
I think the mid to lower level D1s don't have the resources, experience and expertise that many of the top D1 programs possess but that doesn't necesssarily mean they have a win at all costs mentality. Some low to mid-D1 programs dilute their hands-on coaching by wearing many hats. For example, a head coach who doubles as a pitching coach. I just can't get on board with that. As @Consultant mentions, pitchers are special but they aren't china dolls either. Head Coaches don't have the bandwidth to work with every pitcher every day and do all the other things (fund raising, recruiting, etc..) they should be doing for their program.
Thankfully, my son's mid/low D1 program had an excellent pitching coach, strength & conditioning coach, nutritionist and resources available to help them succeed. In my 4 years of following my son's D1 program and all the programs in his conference, I never once saw or thought a pitcher was over used. My son came up the way most freshmen pitchers do. He had a great freshman Fall. He got a non-conference appearance (against #1 ranked team) early in the Spring, and did very well. This got him noticed, and he was starting when conference play began. He never pitched or travelled for mid-week games, and he knew he was getting to be on the bump on the weekend. There was no deviation from that pitching routine in any way.
The potential for abuse in college baseball is there, but I think it is more likely to be someone in the D1 P5 bullpen. My former neighbor was a D1 P5 pitcher at a high profile university. He bounced between the bullpen (setup, closer, long relief) as well as a starter during his sophomore & junior years. Senior year he was exclusively a starting pitching. There were a few pitchers on that team that I thought were overused, but I kept that to myself. If you take the Fall season + regular season + conference championship + regionals + super regionals + CWS that has the potential for a lot of pitches thrown. He did all of that. I believe he also played summer college baseball too. From my perspective, this D1 P5 situation is more likely to be an issue than a low to mid-D1 program situation.
As always, JMO and experience.