Are you saying your Fix.php will be executed every time ANYONE comes to the site?
Yes, which is why you only let it run long enough to clear out the excessive entries, and then delete the file. You don't *leave it there*, you run it only once and then remove it.
The purpose of the fix.php is to clear out all those excess cron entries. That's what that code does.
Fixing the taxonomy.php file will prevent new jobs from being created. Running this code will clear out the invalid existing jobs. Then, problem solved. It only takes one run. Maybe a minute or two to clean things up, tops.