Do not mess with your home folder. It's like removing your windows system folder. OK?
It's safer to move the content rather than the entire home folder... like can you move your photos or videos or music out of your home folder to somewhere else?
Also you should use du from the command line or get an application that helps you analyze disk usage and see if you've lost space somewhere else. Here's an example:
http://www.landsbert.dsl.pipex.com/diskspace/
You can move your home folder perfectly safely and easily.
http://www.macosxhints.com/article.php?story=20071025220746340
I run my setup with the home folder on a different drive to my boot volume. Works perfectly.