If you want all your formulas throughout your moodle site to be in a fixed color different from black, then it is easy to recompile mimetex to achieve this. For instance if you change the following line in mimetex.c:
GIF_SetColor(1, 0, 0, 0); /* and foreground black */
GIF_SetColor(1, 255, 0, 0); /* and foreground red */
and recompile mimetex, this would make all formulas in your moodle site come out in red.
It would not be difficult to make some further changes in mimetex to allow different formulas to come out in different colors.
On the other hand, if you wanted to have multicolored formulas (different colors within the same formula), then this would require extensive changes in mimetex.