You're not storing patient details in VC...... Right? Maybe show him that you can run svn even on his own machine... Anything... Anything is better than not using something
I've work with HIIPA and VC. No issues, as long you do not store patient information within the source code, I cannot think of any reason why you would need to do that...
Did the CEO give a reason? I'm a bit curious based on it being billing and HIPPA. Also, are you rolling your own EDI import/export?