Simply add a starbase "Special" project to liquidate assets. This will produce a quantity of "Starbase Provisions" that can be used on any starbase project. After cooldown, the project can completed with a "Claim" button, just like the reputation items. The result is a reduction in the starbase xp and/or provisions, and a stack of inventory items.
It could be more elaborate, with different liquidate projects to emphasize specific resources or eng/sci/tac XP.
I assume the provisions would be bound to account, at least. I suppose access to the Claim button should be limited to members who can add projects.
Exactly how much a provision is worth can be done in a variety of ways. There could be different provision flavors - credits, dil, doffs, commodities, gear. There could be only 1 type that provides a fixed amount of each resource type, no change given. Alternately it could work by a cost calculation.
Doing it this way would allow fleet members to take a share and part ways. Of course it is up to the leaders to manage the process fairly, but it would be more flexible than a straight merge.
I have the same problem, and saw the need for something this a long time ago. We are trapped in our fixer-upper starbase. I wonder how many players have just cut their losses and walked away. I certainly would be interested, even if there was a significant cost incurred.