I can't think of any rental apartments out at the beach, you're right - the majority of the property out there is vacation rental. But as someone that went to UWF, I really think your best bet is to find something closer. The traffic can get to be a pain going up toward the University area. I used to live by the Navy Hospital, and later by the back gate of NAS and that commute was a killer some days. If you're a full time student, you would be saving yourself some sleepy commutes, brake pads and gas.
If you really are adamant, Perdido has some very pretty property and I knew some LTs that lived out there. Expensive, and very much of a drive if you want to go to the mall or bar crawl, which would be some serious cab fare. If you live in Perdido count on a good 40min commute to the mall, a bit more for UWF. If you live in Gulf Breeze count on 40mins to 1hr. I had classmates that had family out there, but lived on campus/close to campus. Governor's Gate, Kings Mill, and the Fountains are the college crowd apts near UWF.
There are some high rise condos called Portofino, but those are pretty far again, and may be bought out by vacation rentals by now.
Hope this helps some!