Fewer options is almost always better, all else being equal. When it comes down to something like this (upwards vs. downwards) that doesn't affect the drawing or its appearance on the screen, and doesn't limit what's possible or convenient with Inkscape, then consistency with the standard should be (as it has been) the only determining factor.

For new users who expect it to work the opposite way, an option wouldn't really help their first impressions or their learning curve.

For old users who are used to an existing way of working, it's not worth keeping around options to accommodate everyone's old habits. 

I'm sure we could find people who would like to see every possible combination of axis orientations possible (for one reason or another) -- imagine if we had an option for each one.

Just my thoughts,

Bryan