I’m confident given my statistics and everything that I have a roughly 50-50 chance of getting into my top school next year, assuming nothing substantial changes in my life. However, if I don’t get in, there really isn’t another college with my program that I want to go to. I’m fairly certain that if I join the military, I’ll come back with a stronger application.
Some things:
I plan on doing ROTC/serving otherwise, even if I get into my top school.
My biggest worry is that my app will be looked unfavorably if I reapply - does this happen?
If you were to reapply after completing your term of service, you would be a completely different applicant than you had been as a high school student, and you would be evaluated then within your new context. You won’t be automatically rejected because you had applied and been rejected before. And please do remember that by the time you would be applying at that future date, your educational goal may well have changed and this particular institution might not even be on your list any more.
I would encourage you to continue to look at other college options. This one place may be your far-and-away favorite today, but you have time to identify some other options for yourself. Be sure to have a back-up in case your other plans go awry. For example, if you should have a health surprise that would prevent your enlisting, or that would get you sent home permanently half-way through boot camp (I know people who have had those experiences), where could you be happy studying?
Entering military service as an enlisted recruit would be different from entering military service as an officer recruit through ROTC.
There is more than one right school for everyone. Do the work to find other schools that have programs you are interested in.