I am 4'11", much shorter than you wife. This is what I have:

A Trek Madone road bike with a 43cm frame and 650 wheels, no longer available.
A Terry bike about 10 years old, steel, with a 24 inch front wheel and 700 on the rear. A really nice fit. I use swept back Sparrow bars on this bike. Unfortunately, it is no longer made. The closest probably would be the flat bar Symmetry, but it isn't that close.
A Cannondale Quick4 hybrid. This bike is one of the few hybrids that offered its smallest size with 26 inch wheels. I think this bike may be too small for your wife. It fits me perfectly.

If she is looking for a hybrid or a flat bar road bike she may consider:
--The smallest size in the Specialized Vita. This has 700 wheels but is a pretty small bike and I can ride it, though I prefer my even smaller Quick.
--The smallest sizes in the Trek FX, try the 13" and the 15"

If she is interested in a road bike the Terry Symmetry still offers 650 wheels and comes with 28 width tires. The very smallest might even have the 24 on the front and 700 on the rear. The Symmetry comes with both a flat bar option or a drop bar. BikesDirect had some sizes for significantly reduced prices. I had a 44cm Symmetry with drop bars and 650 wheels for a while. It was a bit big for me and I sold it. It was fine when I used an extra short stem. I can't remember if there were mounts for a rack.

The Specialized Ruby in a 44cm is pretty small but no rack mounts. Jamis Endura also has a 44cm bike. This bike is carbon, nice and light, has rack mounts, and will take 28 tires. I can ride it and experienced no toe overlap. But it was a hair to big for me. Both the Jamis and the Ruby have 700 wheels. Felt and Trek's offerings with 650 wheels are no longer available, but you might be able to find them used. The Trek Madone (carbon) and the Trek Lexa (aluminum) used to be offered with 650 wheels. The largest tires they will fit are 25s. I use 23s on my Madone. Neither had rack mounts. The largest 650 tires that are currently made are 28s, and Terry sells them for their bikes.

Surly and Salsa have a couple of possibilities. The Salsa Vaya in the 50cm size (measured different from other makers) is actually small enough for me, though it is a stretch on reach. The Long Haul Trucker in the 42cm size also fits if I use a short stem. Both take 26 inch wheels. I am building up a Long Haul Trucker using extra light wheels to lighten the bike up a bit.