My own experience of college was pretty similar. I came from a solid distance background; the college coach was an ex-400 and 800m guy who believed in super-low mileage and hammering short intervals with tons of rest. I thought the program was stupid, so I half-assed all his workouts, and tried to cut down the rest whenever he wasn't looking. Not surprisingly, I ran like crap for my first two years. (I'd run 4:02 for 1500m in high school; in my first two years of college I ran 4:04 and 4:02.)
I didn't want to transfer, and being part of the team was important to me. So finally, after my second year, I decided I'd quit worrying so much about doing the "right" program. I showed up for practice every day and did what the coach asked, as hard as I could. I ran 3:44 as a junior, and 3:42 as a senior, and I also ran some decent 800s (I'd always thought I had no speed and needed to move up to the 5000).
So do I think my college coach was right after all? Definitely not. I think his program was short-sighted and didn't set us up well for running rounds. BUT I also realized that believing in what you're doing, rather than undermining it with your doubts, is more important than the details of exactly how much rest you take or how long the intervals are.
That doesn't mean I stopped thinking or caring about what we did. I still did more mileage than the coach realized, and I'd adjust workouts whenever possible to be more aerobic. But I stopped wishing I was somewhere else and just tried to take advantage of the situation I was living in.