Had a talk with my recruiting officer (let's call him Major) at my AFROTC Det about applying to USAFA yesterday about pretty much this topic.
First of all, MullenLE is 100% correct. However, I can expand on his points.
Major said that there is no aspect of 'possessiveness' from AFROTC cadre towards their cadets, especially for AS100 (freshman) cadets. There is even a chance that your Det/CC (the officer nominating/competing you) will be an Academy alum. Their job is to qualify you for a commission in the Air Force, and while they could possibly prefer AFROTC over AFA, they don't really mind HOW you commission, as long as you are on a path towards commissioning. And besides, there are even transfer programs between AFROTC and AFA. There's zero animosity between the two commissioning sources, at least from a cadre standpoint.
Although, one thing I will say is that going into AFROTC with the MINDSET of wanting to "ditch their program" is a surefire way to either not get a nomination from them or to get disenrolled from the program. I won't spoil AS100 year for you, but pretty much the only thing cadre judge about you is your attitude towards the program. If you seem checked out cause you have your eyes on AFA, you will find that cadre AND the POC (upperclassmen) will rank you poorly. Which directly affects your chances at getting the AFROTC nomination. You won't be "using" them as a way to get a nomination, you will be SHOWING them that you're WORTH a nomination.
2. DoDMERB doesn't render waiver decisions. AFROTC/USAFA make those decisions.
One of the biggest memes in AFROTC is the omnipresent threat of DoDMERB. You can't escape it, and it takes significantly longer for AFROTC cadets that didn't happen to get a DoDMERB clearing due to an AFA application or a scholarship. If you have a health problem that requires a waiver, email your cadre SOONER rather than later.