They would've had to use the A6X, and since no other devices would've been using that chip as well, it was most likely more cost efficient just to move to the A7, so they could manufacture a single chip in a high quantity for both iPads & the iPhone 5s.
It's probably easier for Apple and software developers to have fidelity across the product line. Most of the cost and hard work is related to developing the technology. Stamping out an A7 processor isn't much harder than stamping out an A6X (maybe even easier). Cost wise there isn't much savings either since an A7 processor cost $19 dollars a piece.