When running KSP, even while I'm still on the ground in Mission Control or the VAB, my mid-2011 Mac mini (2.3 GHz Intel Core i5, 8 GB RAM, Intel HD Graphics 3000 with 512 MB) appears to make serious attempts to follow my constructions into orbit - the CPU fan is running on full power all of the time, and I am worried about the long-term effects of the heat stress. What are the most effective ways of lowering the overall load that KSP produces while still keeping it playable?
I've got a MacBook Pro 15" 2013, and its fans are also running at highest speed while playing KSP (and other games) and a specific spot (CPU or GPU below?) is getting very hot. But in the 160+ hours I've played KSP, nothing has happened apart it being very noisy (add several hundred hours of gameplay in other games as well).
The Mac Mini (like most modern computers) has a built-in heat protection: if it runs too hot for some reason, it will shut down before it's damaging itself. Long term damage can still occur, though: for example, some MacBook Pro 2010 machines ran into issues where the GPU's contacts faulted due to long term heat stress (actually, mechanical stress: constant heating and cooling, thus expanding and contracting by tiny amounts, caused the stress). The fix is to bake its logic board in an oven (really! I needed to do that with mine as well and it fixed the issue).
So you're right to worry about long-term heat damage, but I wouldn't worry too much about it. I haven't found anything about long-term heat issues with Mac Minis. But you can probably help your Mac Mini to stay a bit cooler anyway:
You can open your Mac Mini and vacuum it: remove all the dust that might have piled up. That usually improves heat dissipation. Depending on the amount of dust, it might not make any difference at all or it might make a huge difference (everything was clogged). Also, make sure the vents aren't blocked and that the device has enough "breathing space" (don't put it confined spaces) so the air can actually transport heat away.
On the software side, you can lower the resolution and turn off or down at graphic related settings. My gut feeling is that you probably can't keep the fans from spinning audibly this way, though: KSP requires a lot of CPU power as well.
But as I said earlier, in the end I wouldn't worry too much about the fans running: they're just doing their jobs and it doesn't look like the Mac Minis have long-term heat issues.