I think the base closings and realignments will be decided more or less independently of how the nomination process goes down. If they can make a case for keeping the bases open, then they will be.
There is always and argument that a bases should be kept open. For example, a "consolidate operations" is more efficient. So - Snowe and Collins fall in line on Filibuster, they make a "consolidate" argument in favor of Kittery, which takes hold. Kittery will win out over Groton, just in time for reelections in 2006.
Just my SWAG.