I've experimented with a few ways to wear skirts on bikes, since pants that fit a hard to find.
1. Shorts under skirts. Tilt the bike down and step over it. This does not work with pencil skirts or jeans skirts. I change out of cycling shorts & into regular underthings at work. This works very well with knit skirts, and is only possible because I work for a very flexible non-profit.
2. Ride in comfort, pack a change of clothes. There are multiple ways to do this, as in drive in with a bunch of outfits on Monday, change when you to work...works best with showers and changing rooms. Not always so good in the rain, as you can arrive quite wet. Helmet covers are very helpful in maintaining dry-ish hair.
3. And yes, they DO make "girls bikes," AKA step-thru frames. Felt, Electra, Raleigh, Giant, Cannondale all make commuter-friendly step-thru frames. (As do Pashley and Fuji). I would love to link to all the sites as I did a lot of research on this earlier, but I have to go run errands.
If you do go for a step-thru, you should include fenders in the wish list, and ideally a skirt guard. European bikes often have these-- they keep your skirt from getting caught in the rear spokes.
Jean skirts and pencil skirts are still not so great, even on a girl's bike, at least IMO.
Shopping for a new bike-- way fun! Riding to work looking & feeling great-- even better.