If you go through the DVD forum (
http://quantumleap-alsplace.com/forum/forumdisplay.php?f=9) there are a lot of threads that address this.
Simply put, it was cost prohibitive to put the original music on the DVD's. That would have meant Universal licensing the music (which adds to the cost of producing a DVD set). The extra cost of licensing would have then been passed on to the consumer. Quantum Leap is going to reach more of a niche market than a broad market so it just didn't make economical sense for Universal to go through with the licensing of all the music.
If you're wondering what the cost difference would have been compare this. Season 1 is only 8 episodes long and contains all of the original music. It lists on Amazon.com for $31.99. Season 2 is 22 episodes but has music substitutions. It lists on Amazon.com for $38.99 - only $7.00 more despite being more than twice as long as Season 1. Had Season 2 (and subsequent seasons) contained all of the original music, they likely would have retailed for double or more than double what the cost was without all of the original music. That may have been more costly than what the consumer was willing to spend.
As to Universal obtaining the music licenses necessary and reissuing the DVD's with all of the original music, I'd have to say it's highly unlikely that that would happen with the economy the way it is. It's even less likely today that someone is going to be willing to spend that much money than it was a couple of years ago with Universal first released the DVD's.