You can shut off the folding any time by hitting the triangle button and select "quit folding" in the menu that comes up. The current work unit will pause and resume where you left off when you fire it up again. Folding only runs when the PS3 is sitting completely idle. It does not run in the background while gaming, watching a movie, etc.
You can set the Folding program to start up after 10, 20 ir 30 minutes of sitting idle. Just hit triangle when highlighting the Folding icon in the Internet section of the XMB and make your choice.