My wife is on the small side at 5' 2". Finding good bikes for short riders is challenging. A lot of companies pretend to make a small bike with a short TT, but then simply make the seat tube angle VERY steep, which effectively makes the top tube longer... defeating the reason for the short TT in the first place.
She's raced CX for a number of years and has several bikes.
He favorite production bikes are: the Ridley X-fire in a "41". It has a nice short TT, normal seat tube angle, and a very short head tube. So, she can run a 100mm stem and the bike handles great.
Close second is the Specialized Crux. You're wife would want the 46.
Custom is an option as well. My wife has two Speedvagens, loves them. But, super $$ and the wait on a custom frame can be long.
We're probably going to sell the Xfire this year, to fund the purchase of a new one. If you are interested in a great deal, let me know.
Here's a shot of how the small bike looks. As you can tell, the seat can go a
lot lower and the stem has a number of spacers under it. This frame can accommodate really small riders.