There are several good over/under arm strengthening programs out there that work well. If throwing 100%, I would agree that most weighted balls are too heavy. The system I've used for overhand and pitching underhand , uses an 8 ounce heavy ball and a 5 ounce light ball. A regulation 12" softball is between 6.75 and 7 ounces, so the 8 ounce ball is just slightly overweight. Of course never throw hard until fully warmed up with a regulation ball. The system starts with 12 throws as hard as possible with the weighted ball, a 2 minute break and 12 hard throws with the light ball, a 2 minute break then 12 hard throws with a regulation ball. Alternate 60' one day and then 120' the next day three days per week. After two weeks, increase the reps to 18 each, then 24, 30 and so on up to 48. By the time you reach 48 reps, throwing speed will increase at least 4-6 mph for most girls, and I've seen as high as 10 mph. This being said, a girl that plays a lot of ball and throws all the time may not see those kind of increases, but it will definitely make her arm stronger and less injury prone. There is also a series of shoulder stretches and excercises that go along with it. When used for pitching, the light weight ball is great because it is very difficult to control and really helps with the proper release point and accuracy as well.
After three years of doing this with 15 - 20 different girls starting at 12U, I have not had one complaint of a sore arm or shoulder resulting from this program.