You hit the nail on the head. If you're the second best team in the sectional, you've more than likely put in the work to get yourself there. It should be rewarded. Instead, the two worst teams in the sectional match up against one another and one earns the right to move on while a program that worked harder packs their equipment and calls it a season.
Now, there's certain someone who'll come on here and accuse me of questioning the work ethic of certain high school football programs. It's like anything else in life and it's a lesson learned. The harder you work, the higher the performance. That's true with anything in life, sports or otherwise. There should always be a reward for performance, but the IHSAA doesn't see it that way with the blind draw. My guess is it's just "easier" to pull names out of a hat than it is to determine a seeding method.