Is it as easy as going to the save folder and copy pasting? I tried that before and it didnt work. And if I have the fixpack installed, uninstall the game and reinstall, would that save game be corrupted?

Strange that the copy pasting didn't work. I've done that before and it always worked for me but that was without the fixpack or any other mods installed. I can't see how the installation of a mod would impact the copy/paste process. Try copying the entire saved game folder - folder AND the contents all in one copy paste.

In regards to the game corrupting....

If you have something referenced in your save game file that doesn't exist in the installation, I can see that there would be problems.

Just make sure that if you remove BG2, note exactly what you have installed. When you go to play your backed up game again, make sure you have every patch / mod installed that you did when you first backed it up.