Homemade CPU and 8bit computer with discrete logic
old.reddit.com
old.reddit.com
As you said, from an educational standpoint, most students(some of my colleagues last year at least for example) were kind of missing that you are not "programming" an FPGA, but rather describing the circuit. Furthermore, when you add conditional statements(if, else if) , you completely lose track of how it's being implemented and therefore you are not really learning digital design(in my opinion).
Of course doing everything with discrete logic also has its disadvantages, like being time consuming and expensive, but when doing so, you really know how every digital block communicates with the other and learn true digital design.
Anyway, I think both discrete logic and FPGAs should be taught in college. The former as an introduction and the latter as the standard industrial way of doing things nowadays efficently.