While I would agree Composer has its issues, it isn't going to help with the current situation to just stop using it.
That said, you do need to be careful with Composer's snapshot process. I almost never use it unless I really need to, and when I do I often go through the capture results with a fine tooth comb to be sure there is nothing in it I don't want. Especially remove any home directory stuff if you don't plan on using the FEU/FUT options.
As for your current dilemma, I assume this file/plist/whatever is in a known, consistent location? If so, here is the general syntax you can use in a search and destroy type script to find it and remove it in any local accounts. As always, there are several ways this can be accomplished and this is only one. Obviously, modify this to your needs and test it out before pushing, since you're deleting files. You don't want to make a bad situation worse by nuking the wrong stuff.
#!/bin/bash
targetFile="/relative/path/to/target" ## Exclude any home directories, just the path to the file from the account, i.e, /Library/Preferences/preference.plist
for user in $( dscl . list /Users UniqueID | awk '$2 > 500 {print $1}' ); do
userHome=$( dscl . read /Users/$user NFSHomeDirectory | awk '{print $NF}' )
if [ -e "$userHome$targetFile" ]; then
rm "$userHome$targetFile" ## use 'rm -R' if the target is a folder
echo "deleted $userHome$targetFile"
else
echo "Nothing found to delete for $user"
fi
done
