As I understand then ... Delta, which owns (?) Comair, should follow your logic of "The contractually proper thing for Delta to do would be to incorporate those RJs into Delta mainline and transfer their pilots from the larger jets to the smaller jets." I tend to agree if 1. Comair and Delta are all the same family now, 2. The "smaller airplane smaller paycheck" policy remains and 3. If the big jet guys can transfer to smaller jets, then the small jet guys should be able to compete for the big jet seats. In the end I suppose flying for less money on a smaller jet (but still good benefits) beats not flying and/or no money.
On the wider screen though it seems that there is a tendency in the industry to put a great deal of blame on "intransigent unions" and "route grabbing RJs". From the sidelines it looks like the small jets are bringing customers to the big guys and are doing it profitably. Is it a heavy bureaucratic/administrative structure that prevents the large airlines from moving those same customers on the long routes?
Seems like a tangent to the original topic but I wouldn't mind following it.