Shorts may alleviate the problem some (and yes, girls do go commando too, although you don't really have to as long as you don't tell UnderwearNazi about it
). However
shorts will not solve the problem. Neither will gel pads. Gel pads are just gimmicks. Shorts are useful, but not for this sort of thing! Their function is to prevent chafing and minimize air resistance and stuff like that. It's not to fix saddle problems. If you're not comfortable in the saddle wearing regular pants, the problem won't go away with the purchase of shorts. You need to adjust the saddle - or buy a new one if no adjustment yields a desired outcome.
I've had this trouble myself with some seats. It can be excruciatingly painful. In my case every time the cause of the problem was the fact that the seat was too narrow at the back. This way my sitbones (the two bones in the bum we sit on) were not supported by the seat (girls' sitbones are typically wider spaced than men's to allow for childbirth) and so I was sitting on my soft tissues. OUCH is the only printable word that comes to mind! So one thing I would check out is whether the seat is wide enough. Does she feel her bum is being supported by the saddle on both sides?
In some cases the problem is not the width so much as the angle of the seat. Ideally a seat should be perfectly level. If its nose is pointing up, it's bound to put a lot of pressure on certain parts of female anatomy and cause discomfort. Some women angle their seats down a bit (just a couple of degrees) so that the horn is out of the way. This solves the pressure problem, but sometimes creates a new problem of rider sliding down the seat and thus putting a lot of weight and stress on the arms. Bad situation.
You may also try to move the saddle forward a bit to see if it does anything.
So if you find that saddle adjustment doesn't solve the problem - it's time for a new saddle. Which one? Well, firstly it's gotta be a good width: not too narrow and not too wide. A bike shop should help you with that. Also, an anatomical cut-out (basically a hole) in the front of the saddle often works for women. Some companies (notably Terry) make women-specific saddles taking anatomy into consideration. I personally am very happy with my Specialized Body Geometry Comfort saddle (men's version).
Hope this helps.