It might be better to try persuade it not to write them in the first place...
- Open Terminal.
- Execute this command:
defaults write com.apple.desktopservices DSDontWriteNetworkStores true
- Either restart the computer or log out and back in to the user account.
From Mac OS X v10.4 and later: How to prevent .DS_Store file creation over network connections which apparently has never been superseded or indeed maintained for a long time, but is still the recommended way.
You might also find this interesting - Got a Mac? Prevent OPSEC leakage by cleaning hidden OS X files from USB drives The recommended freeware from that report CleanMyDrive claims to be able to handle network volumes too [I'm just testing it myself so have no results as yet, but reviews are good on the app store]