I am aware that this can be done with image manipulation, though this all takes time to do, in which we could be doing something else.
Seeing that blender is the odd one out in this respect as most applications use y for up and down, i think its not to unreasonable to ask for this...after all blender is trying to integrate its self towards game creation now and flipping channels just adds to the awkwardness of its use and many users wont know about this fix.
I shouldn't be that hard to implement and would save time and reduce the steps needed to create a usable map.
Also the map would need to be re-normalized to make sure that all the image normals are pointing in the right direction, otherwise this can cause problems with the normal map and with the specular map that it is possibly being used in conjunction with.