Why can't you simply mark what changes you want to have in a commit using "git add " (or even "git add --interactive", or "git gui" which has option for interactive comitting), and then use "git commit" instead of "git commit -a"?
In your situation (for your example) it would be:
prompt> git add B
prompt> git commit
Only changes to file B would be comitted, and file A would be left "dirty", i.e. with those print statements in the working area version. When you want to remove those print statements, it would be enought to use
prompt> git reset A
or
prompt> git checkout HEAD -- A
to revert to comitted version (version from HEAD, i.e. "git show HEAD:A" version).
