I disagree that they won’t do this in the fleet. I can’t tell you the number or HR, supply, SWO, sub, intel, IP officers from the Navy who served in Individual Augment roles and did tours running convoys and other things in Iraq and Afghanistan. Pilots do tours as FACs and EOD, SEALs do this stuff all the time. What about if your DS is a boarding officer on a ship who is leading others... climbing up and down nets, leading teams boarding ships and possibly engaging with bad folks. Subs send officers to dive schools all the time. That is an intensive school. Being in top shape can be the difference in life and death or them saving one of their sailors.
Cross Fit... if not done right can be bad. Mids getting hurt is not a good thing. Some senior Mids in the Unit can speak to the Officer about their concerns over injuries. It could be lack of being in shape is leading to these. It could be poor form. The bottom line is this about pushing them mentally and physically, making decisions while exhausted and learning that they can push themselves further than they think. Being honest, an engineer major has nothing to do with this. When they get to the fleet in whatever their role is, no one cares their major is. Sure it’s a culture clash between Navy and Marine Corps, but they will encounter all kinds of leaders in the fleet that they have to adapt to. All the stuff you mention seems like standard training that every Mid at USNA encounters all the time regardless of major or desired service selection.
I apologize if my response comes off as harsh. It’s not intended to, but this is his thing to deal with. I have spent my fair share of time in combat zones and seen what happens when people are out of shape or are mentally weak. Regardless of rank, branch or MOS/career designation, you never know where your career will take you. He has a chain of command and he can express concerns via them.