couldn't find an answer anywhere.
so here's a quick workaround:

in /etc/X11/XF86Config{,-4}
Section "ServerFlags"
 Option "AllowMouseOpenFail"  "1"

and add a second mouse:
Section "InputDevice"
        Identifier  "Mouse9"
        Driver      "mouse"
        Option      "Protocol" "ExplorerPS/2"
        Option      "Device" "/non/existant"
        Option      "ZAxisMapping" "6 7"
EndSection

then select it as coredevice:
Section "ServerLayout"
InputDevice "Mouse9" "CorePointer"
InputDevice "Mouse0" "SendCoreEvents"

back in x:
$ xsetpointer mouse0
$ xset m 2 1
$ xsetpointer mouse9
$ quake3 +set in_dgamouse 0

now it will be accelerated *even when moved as slow as you possibly can* - so in effect it will be nullyfied - now just lower your sensitivity.
this happens because q3 initializes the mouse to accelerated state when it starts, q3 will now initialize the wrong eg. non-existant mouse.

if you wish to change mousesetup from within x, you must naturally swich to mouse0 using xsetpointer, since otherwise you will be setting up mouse9 (using xset m or xmodmap or)... 

/Allan Bruno Petersen


Update:
$ quake3 +set in_dgamouse 0