No, I don't think UConn football is respected. Louisville football is respected now, but a few years ago it was in CUSA and worse than mediocre. I think the current perception of UConn football is just as changeable as Louisville's past perception was. There is a predominant "what have you done for me lately" attitude. And if UConn were to go 13-0, as you so presciently predict, we would soon rise above Louisville in people's football perception.
Regardless of that, it's a short-sighted attitude to grade universities and athletic departments on recent performance of the football team. The ACC just did that, but it was under great stress. Also, it was choosing between two athletic programs very similar in stature, so small considerations could tip the balance.
The B1G has smarter people thinking about realignment from a secure position and able to take a long-term view. They also have a different model which rewards state flagships with strong loyalty and values basketball more than ESPN does. (ESPN has a ton of pro and college winter sports inventory and won't pay up for an additional bit of college basketball; the BTN has no pro sports inventory and gains great benefit from quality winter sports.) Given that the ACC has sold itself lock stock and barrel to ESPN, UConn isn't as valuable to them, because our quality sports aren't needed by ESPN. But UConn is extremely valuable to the B1G, for its basketball, multiple quality sports, domination of Connecticut, reach into New York and New England, and football potential.
What I'm saying is that, among the decision-makers I care about, Louisville's recent football success won't matter a damn. Think about it from the B1G's perspective. They would never in a million years consider Louisville, even if Louisville won a national championship in football, or ten national championships. They will consider UConn, even if our football team stays mediocre.