Hi, all. I've encountered the same need and found some solution.
What I did - added website to my solution and configured HS build profile to generate output to the website's folder. Before rebuilding HS project I need to check out the website, then generate help, then refresh folder structure for the website in solution explorer (if files were added to the folder it's handled by VS and it automatically adds them to source control). Then just check the folder in. Now I can even deploy my help separately or add the website's output to setup project. That's nice.
It works for me but it still has limitations and inconvenience (for example everyone who builds help must reconfigure build profile, VS doesn't seem to handle deleting files from website's folder - only adding etc.). So I would join burkni with requesting some additional integration with source control for HS projects output.