If you back up your current Divinity2.exe (non-patched one) you can safely install the patch. After you done collecting data, just replace new Divinity2.exe with the backup'd one. Oh, and delete ..data/win32/packed/Patch.dv2. The patch will be "uninstalled".
Does doing this affect any of the changes from the patch, including the new menu options?
I don't understand the question.
I did the .exe swap, as you suggested. It allowed me to play the patched version of the game without any graphic errors. However, I do not have the advanced video options, or the ability to change the setting to nightmare mode. So I was weary the .exe swap might affect in-game patch changes as well. After playing through most of Broken Valley though with it patched it seems the fixes are still working, and the .exe swap only affects the menu changes.