Make "bin/config set --database ..." resurrect deleted values

Summary:
Fixes T12409. Config entries may be marked as "deleted", and bin/config set --database doesn't un-delete them, so the edit doesn't do anything.

The "most correct" fix here is to swap to transactions so we run the same code, but just fix this narrowly for now since it's one line of code.

Test Plan:

• Set maniphest.default-priority to 123.
• Deleted maniphest.default-priority from the web UI by deleting all the text in the box.
• Before patch: bin/config set --database maniphest.default-priority 789 had no effect.
• After patch: bin/config set --database maniphest.default-priority 789 worked.

Reviewers: chad

Reviewed By: chad

Maniphest Tasks: T12409

Differential Revision: https://secure.phabricator.com/D17506