The first thing is style. There are the conventional step through/lady frames:
which have the same sort of clearance as step through frames but are stronger. Then there are women specific geometry bikes.
In general, both mixtes and step through bikes are inferior to the standard diamond frame due to reduced strength and stiffness, increased weight and less mounting points for stuff. (Of course, you need to do reasonable comparisons in this case). And they became a lot less common once people stopped riding bikes frequently in skirts.
Trek among other major manufacturers offer women's geometry bikes (Trek marks theirs WSD, Specialized uses slightly different names, and Giant uses LivGiant or something). These are usually variations of the corresponding men's model with a lower top tube. Probably not good for a full length skirt.
Soma also sells some mixtie frames (their buena vista, for example), which you could spec up at your LBS. Velo orange also sold one until quite recently it seems, but if you dig through the manufacturer's websites, you'll find things like the Trek Belleville WSD, Specialized's Globe brand, etc. Rivendell (a high quality boutique manufacturer) sells their Betty Foy as a frame set, but it is a quite expensive one.
Since this is really a shopping question (and is likely to be closed because of that), we should note that your bike shop can help you with bikes available in your market, along with the important bike fit problem. If you ask them for a mixte frame (or even a step through frame) and tell them what its being used for, they can likely find something for you or order a quality frame and build it up with other parts.
Finally, note that many frames from the 70s or 80s are still just fine - if you look at your local used market for a mixte or step through frame/bicycle from that era, get it checked over and tuned up at your LBS (which may involve replacing a bunch of parts on it, admittedly), you can likely get a pretty good quality frame for cheaper than buying one new.
Alternatively, convince your wife to wear pants to cycle to work (if you're cycling 2 hours a day, this is likely to be more comfortable anyway) and use a diamond frame, and then change at work.