If you send them to /tmp you'll also need to purge the files from /tmp as well eventually otherwise you'll end up with a ton of /tmp files and things will start slowing down.
What you want to do is simple, open the directory for /images/thumbs/*/ and iterate through all the files, checking the file status for either the creation date, and purge anything > 90 days old.
Not sure what you mean by level 1, 2 or 3 deletions, file deletions are file deletions., either move them to /tmp or unlink them.
I do something similar to my thumbs but do it on the command line with a couple of simple commands, assuming you're using Linux. First I run a script in PHP that queries the database to find everything currently in use and 'touches' all of the currently used thumbs just to update their current date. After that, I simply purge all files that don't have the current date after running that script.
For instance, for each file being used I shell out and update the date like this per image:
touch -m ../../httpdocs/thumbs/imagename.jpg
Then it takes two simple commands to purge all unused images:
ls -l ../../httpdocs/thumbs/ > allthumbs
rm -f $(grep " Feb 11 " -iv allthumbs | grep "jpg" -i | awk '{print "../../httpdocs/thumbs/"$9}')
Replace " Feb 11 " with your current date in the above script and purge away.
Be careful however, run the GREP portion of that script first to test it before adding the "rm -f $()" wrapper otherwise you could inadvertently blast all of your thumbs by accident.
Requires adult supervision.
