Open in_win.c, find the declaration of newmouseparms. It should look like this:
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static int originalmouseparms[3], newmouseparms[3] = {0, 0, 1};
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static int originalmouseparms[3], newmouseparms[3] = {0, 0, 0};
OK, so what's going on here?
Basically these mouse parameters refer to 3 factors that control how the mouse behaves. The first two are acceleration thresholds, and the third is an acceleration level. Setting them all to 0 replicates the behaviour of DirectInput exactly, which is to completely ignore the settings in your mouse control panel and just give flat unaccelerated input.
For bonus points you can cvar-ize them; that's an exercise left to the individual.