You can use sudo for this task. You're going to configure sudoers file in such a way that your cm user which runs webapps gets a permission to run a specific command (rm /your/stray/files) as another user, their owner probably. Something like this:

cm      webhost = (user) rm /your/stray/files
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...and then executing sudo -u user rm /your/stray/files from your script.