I have fired a sub-compact XD-9 and didn't find it uncomfortable to shoot. I'm probably not the best judge of that though (I don't find .44 Mag uncomfortable to shoot either). Still, I don't think you would have any trouble with an XD sub-compact.
Another very good choice is the SIG P239. My brother has one and it is extremely accurate and reliable. The smaller grip tends to fit small hands better as well. Best of luck in your search.