If you create a DefaultDeadBranchStrategy with 0 days to live, and 0 builds to keep, you can easily create a situation where a branch can be deleted while a job on it is active.

When branches are re-indexed, the project will be deleted and interrupt active jobs.

I believe a more appropriate course would be to wait for a branch indexing to run while the project is inactive, a state which once entered it shouldn't leave since the branch was deleted (unless it were recreated).