Helpfully, of course, Subversion allows you to set arbitrary, versioned, properties on your files, so it’s actually pretty easy to store the Finder labels and retrieve them when you want them. Or it would be if there were any command line tools that could read and write them.
Well there are now (download the source code).
Once you have that installed, it’s just a matter of doing
to save your Finder labels as Subversion properties (a change that you can then commit to your repository), or
to restore them after an update.
Or you can do
to see the colour of a label, or
setlabel myfile.txt red
to change its colour to red.
setlabel programs are provided with man pages. The Subversion scripts are not, but they should be self-explanatory anyway.