The vast majority of the attractions at WDW will not require you to split up your group. You can read more about this
here. I will also add to this that some attractions that have vehicles that seem like they would be best for two people can really squeeze in three, if two of them are children. On my most recent WDW vacation, I experienced Peter Pan's Flight, the Haunted Mansion, and the Seas with Nemo and Friends with both of my medium-sized 8-year-old twins in the same ride vehicle with me (and I'm not petite). We were cozy, but it worked. I think this would also work with Winnie the Pooh.
Now that I think about it, there is really only one attraction at the Magic Kingdom where I could see any issue for you: the Tomorrowland Speedway. These cars really do only hold two people and your girls would likely be too short to ride alone. Perhaps you could just skip that one attraction.
As for the child waiting alone scenario, I really wouldn't do that. Cast members are not allowed to "babysit" children. And rarely there are occasions where rides do "break down" or stop in the middle for extended periods of time. I was once sitting on the Haunted Mansion ride for about 25 minutes while a problem was addressed. A child waiting alone could become quite upset in a situation like this.
Again, I can only think of one attraction in the entire Magic Kingdom where you might have an issue at all. So, I'm sure you'll have a great trip!