I dissected the XML file a bit and it turned out to be a XML property list (sort of a XML-based JSON equlivant), so it becomes easier to handle. If the files affected have the same name not counting its extension, some Objective-C can be laid down to change it. Do you have Xcode installed or should I prepackage it for you?
My Setup: Crashplan, OS X 10.8.2, iTunes 10.7 (21)
I am unable to replicate the same issue on my system, and haven't noticed any excess changes or uploads to crashplan on my filesystem after playing music. To be sure it wasn't happening in the background, I ran a checksum on one of my audio files, played the complete song in iTunes, and re-ran the checksum. If something in the file itself had changed, the checksum would be different.
Here are the results:
Big-iMac:Abbey Road dave$ openssl sha1 17\ Her\ Majesty.m4a
SHA1(17 Her Majesty.m4a)= 3aea5150d7b1d21846b6502bac7ccacca44ff0fa
Big-iMac:Abbey Road dave$ openssl sha1 17\ Her\ Majesty.m4a
SHA1(17 Her Majesty.m4a)= 3aea5150d7b1d21846b6502bac7ccacca44ff0fa
As you can see, the checksum matches the second time after playing the song through iTunes. Most of my collection is ripped into ALAC (m4a), so I thought I'd test a standard mp3 file as well:
Big-iMac:One More Night in New York City dave$ openssl sha1 2-21\ The\ End.mp3
SHA1(2-21 The End.mp3)= a223d6fb542bee5191794d0a74f971da19fb9afc
Big-iMac:One More Night in New York City dave$ openssl sha1 2-21\ The\ End.mp3
SHA1(2-21 The End.mp3)= a223d6fb542bee5191794d0a74f971da19fb9afc
This too produced the same checksum before and after playing the song in iTunes. All of the metadata about your library (play count, etc.) is stored in the iTunes Music Library.xml file, not in the mp3 itself so I wouldn't expect individual songs to change. However, it's quite possible that the iTunes Music Library file will need to be re-uploaded since it changes frequently.
Best Answer
afaik since iOS 5 there is no longer a Linux Application that supports syncing Music to an iPhone (there used to be GTKpod)
The easiest would be to install WINE and then iTunes I suppose.