I wrote a first draft of a manual relative mouse mode, in branch "alternative-mouse-input-1.3". You find the new button in the options menu, submenu "Config" (together with the other mouse related options). When you set it to "slow" it should work for you.
With "slow" and "fast" I refer to possible performance impacts. However, It turns out that the new "slow" method actually moves the marble slower. This was not intended. Even worse: Sometimes events are ignored. I reposition the (invisible) mouse cursor to the middle of the window on a regular basis. This generates a mouse motion event (because of cause manually moving the cursor generates an event -- it's not that the program wouldn't know, duh?), which has to be flushed. "SDL_FlushEvent" does not work for me, so, right now, I flush everything, including key strokes that happen in between. And maybe even additional, real mouse motion events, which would be the origin for the slowed down marble.
So, as of now, it's a hot-needle workaround.
Could you check if the "slow"-mode at least works for you? Thank you in advance.