Is there a way to make git rerere work when the resolution is to delete the conflicted file?
As the way it stands right now, No. rerere tries to record previous resolutions based on hunks in each conflicted file. In case of delete, rerere sees it only as no hunks to resolve.
I had problems too when the feature branch includes a new file that doesn't exist in the main branch , but in order to get the feature branch merged into the master and have it work correctly, it requires a small modification to this new file. The git rerere doesn't realize that this is part of the entire merge process and hence never records the changes required.