As previously stated, I would use the one you are best with. Having said that, if you shoot both the same, I would go with the highest capacity. Good placement and enough to take on what you need to until you get to better cover, more ammunition, account for everyone, or get to a long gun.
Since you say a rural setting, I would guess it's you and any family against intruder(s). I assume you have extra magazines and a couple strategically placed for reloading.
I'd go with the 9mm for it's greater capacity if you shoot both the same.