Before you guys edit my posts and claim that I'm over reacting you should try it. I invite you.
Fair enough. That's why I have my Crash Test Dummy™ installation after all.
* Jan disables all other plugins, makes sure he's using Twenty Eleven, download and installs plugin. Configures said plugin. *
Okay, here's the thing and please note that I'm not making fun of you or disparaging you in anyway.
I think you're overreacting.
I just tried it and found that a) it edits my .htaccess file in not the right place and b) puts a nonce in my .htaccess as part of a redirect URL (that's not good) c) it totally doesn't get that my install is in a subdirectory.
Some editing of the .htaccess file and I got past that and I really don't think that's a useful plugin for me.
But I can reasonably say that aside from it being poorly documented and lacking some checks, I don't see how it could have done what you've said.
I even modified a file by hand and compared the WordPress files via
find . -type f | egrep -v "\.svn" | xargs -I{} svn diff {} > results.txt
That's not a 100% thorough check but it's pretty darn close.
Except for the one file I modified, it didn't pickup a single file that was changed and reported (as expected) things like
svn: 'wp-content/themes/twentyeleven-child/style.css' is not a working copy
I just don't see any evidence that that plugin can do what you say it did.