I do this already (and also for /etc) and I can confirm that file permissions are preserved.
With regards to security - it all depends on where you are keeping the subversion database - I keep mine on my laptop, / partitition under /srv/svn.
If the user created it then it will be just as hard to break into as your home folder - your home folder has nothing special besides file permissions.
If someone else has root access, then you're screwed, but then again if they have root access they are probably already browsing your home directory