Equivalent to "git update-index --assume-unchanged" in SourceTree
I just defined custom action for this task.
Make sure the path to git is correct.
Thanks to @RobCroll from the comments, we now have a Windows version:
C:\Program Files (x86)\Git\bin\git.exe (for x64 use: C:\Program Files\Git\bin)
Parameters: update-index --assume-unchanged $FILE
It is quite likely that SourceTree doesn't have a feature for manipulating the index in that way (although I could be wrong, but it doesn't seem to). However that doesn't mean you can't drop down to the terminal in order to issue that command, but continue to use SourceTree for everything else.