Is it possible to use a different program to handle the mouse?

I’m sorry but Mouse and Touchpad seems sketchy. First of all, in its ui, for my mouse there is no sensitivity option, just acceleration. And I prefer to completely disable acceleration, but acceleration 0 is actually negative acceleration; so apparently their ux designer thinks that acceleration 1.0 is how you define raw input? but what’s funny is it doesn’t feel like that, in general i feel input latency and really dodgy tracking using a Superlight 2.0 mouse.

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It’s components of DE (Desktop environment). Currently Qubes OS uses XFCE which is not good in many aspects, including GUI settings (mouse settings in your case). Previously KDE used and supported KDE out of the box, currently only half-dead XFCE. So, you should search XFCE forums, maybe it’s possible. Or maybe it’s possible to achieve using settings for Xorg that is used underneath the DE.