Yes, teams should be 'punished' if you like, for the schedule they actually play. It doesn't matter why the schedule is bad. The committee should be grading off results, not prior years history or thoughts about why a schedule looked good 6 years ago.
Until the committee stands up and puts in worthy one loss teams over undefeated teams with nothing on their resume this will happen on purpose more in more in the future. The SEC isn't punished for their 3 shit OOC games for most teams because they get a pass for possibly having a 4th one that is good and/or the notion their league schedule makes up for it, which it obviously doesn't always do.
Teams shouldn't be "punished" based on schedule. I have no idea what that even means. Teams should be graded based on how they play and what their record looks like. Obviously, a team who goes 8-4 against an SEC schedule should be above a 10-2 Conference USA team. That's not because we are "punishing" the Conference USA Team. It's because based on how they played and who they played, we have every reason to think the SEC team is the better and more meritorious team.
I have no problem with people saying "I think Notre Dame is better than Wisconsin" based on their harder schedule and their relative performance on that harder schedule. That's very different than suggesting the committee needs to "punish" Wisconsin for scheduling poorly.
You are basically suggesting punitive damages for Wisconsin's schedule, which suggests that teams need to be deterred from scheduling poorly. The problem is there is no incentive to avoid scheduling poorly if the team that's punished made an effort to schedule a fair schedule. Considering where BYU was when we scheduled them, I think it's fair to say that we reasonably thought that would be a pretty tough non-conference true road game.
If you want to give actual damages to Wisconsin, go right ahead. Just be consistent and give it Miami as well (for now at least), and don't forget that several teams ranked around us lost to the types of teams we have beaten.