The way I see it Compiz is just a Windows manager so doesn't interact with your running applications other than providing a graphical structure within which to run them as it is a window manager.

I know its not the most reliable source but citing Wikipedia Window Management:

A window manager is system software that controls the placement and appearance of windows within a windowing system in a graphical user interface.

And more importantly:

Elements usually associated with window managers allow the user to open, close, minimize, maximize, move, resize, and keep track of running windows, including window decorators.

This last phrase explains that the options you have with windows managers running are to close, minimize etc. The way I see it, by restarting Compiz you won't tell your current applications to do anything, you haven't given them a specific command by clicking on any of the window manager icons so the applications have no reason to act differently than if you left your PC for a few seconds. You'll just have them idle until they are put back into a window manager (Compiz in your case).

So yes it is safe to kill and restart compiz