I don't use Cinnamon myself - you might want to browse this thread: viewtopic.php?f=90&t=94195
Here's the part that may make you day:
N31L wrote:I had the same issue with the mouse focus also raising the window to the front no matter what settings I made. It took me an hour to finally find the place where the "auto_focus" setting would actually affect the windowed behaviour in gnome.
I had verified that I had the correct settings (in gconf set auto_raise to false & focus_mode to sloppy) but no matter what I changed these settings to, the behaviour remained the same. I downloaded gnome-tweak-tool and made similar setting in the windows section of that, setting the windows focus mode to sloppy... but again, no change in behaviour. I also tried downloading ccsm (compizconfig settings manager) and setting the options there, but that didn't work either.
Finally, I went into dconf-editor (you can download it with 'sudo apt-get install dconf-tools' if you don't already have the package) and under:
org > gnome > desktop > wm > preferences
I found the same settings as in gconf-editor under Metacity. Here I unselected auto_raise and then changed the focus_mode to sloppy.
These settings actually took, and now the focus moves with the mouse -- without also bringing that window to the forefront.
Hopefully this helps.
Seems like a bit of a hassle for a simple wish, but hey, after that you'll know what the dconf-editor looks like.