By the time the T&T is finished, other canals will be under construction. The goal will be to connect the Upper Mississippi and Ohio rivers not just to the Gulf, but to the Atlantic. There will be several termini, including Brunswick, Ga., Savannah and eventually Charleston. Blockading them all will be a bigger job than just occupying Mobile Bay.
You're talking about bloody long canals crossing the Apallations. Is possible but is it practical? Also going to be very expensive so will need a lot of central government money, not to mention gaining control of the land.
As for the freedmen, the President and Domestic Affairs secretary will be quietly arranging land grants out west for those who want to get out while they still have their health.
Crafty. Since the US still has to conquer most of that then they could form a core of 'loyalist', unless they find they have more in common with the inhabitants. Or possibly Congress thinks they will largely get killed off.