dolt fetch --prune doesn't work when sql-server running

see: https://github.com/dolthub/dolt/blob/801a82a3af6e60d688e12238dec22bd5c9ea7e10/go/libraries/doltcore/env/actions/remotes.go#L742

For reasons which are not immediately clear the `dolt fetch --prune` command doesn't seem to actually prune when a sql-server is running. I _think_ the race mentioned in the code above is the reason.

Start with go/libraries/doltcore/env/actions/remotes.go at the linked code near line 742, then reproduce `dolt fetch --prune` while the SQL server is running and compare it with the server-stopped case. Trace the suspected race and identify the relevant existing tests or entry points. Done means remote-pruned data is actually removed while the SQL server remains running.

Written by the indexing model from the issue text.