You could probably work around that problem by using the xset (with the option m ) or the xinput command (set-ptr-feedback). If they work when executed from a terminal you could then put the command into a text file and execute that either manually when needed, or automatically at startup/login. I have not used them on the Pi but on my desktop computer in a similar situation. They are general X-windows programs and should work also on the Pi. (If they are not installed by default, you have to install them first. They should be in the repositories.)
The xset is simpler to use. Here is what the documentation says:
The m option controls the mouse parameters; it may be abbreviated to 'm'. The parameters for the mouse are `acceleration' and `threshold'. The acceleration can be specified as an integer, or as a simple fraction. The mouse, or whatever pointer the machine is connected to, will go `acceleration' times as fast when it travels more than `threshold' pixels in a short time. This way, the mouse can be used for precise alignment when it is moved slowly, yet it can be set to travel across the screen in a flick of the wrist when desired. One or both parameters for the m option can be omitted, but if only one is given, it will be interpreted as the acceleration. If no parameters or the flag 'default' is used, the system defaults will be set.
If the `threshold' parameter is provided and 0, the `acceleration' parameter will be used in the exponent of a more natural and continuous formula, giving precise control for slow motion but big reach for fast motion, and a progressive transition for motions in between. Recommended `acceleration' value in this case is 3/2 to 2, but not limited to that range.
There are probably many ways to execute that command without typing it again. I have it in a text file that I then execute when needed:
It is possible to have many files and then execute then when needed with a shortcut from the panel or in some other way, if e.g. some game needs different settings than your normal desktop use.
http://www.x.org/archive/X11R7.5/doc/ma ... set.1.html
Xinput gives also other options to tweak your mouse, but is more complex to use:
http://www.x.org/archive/X11R7.5/doc/ma ... put.1.html