My guess is that mixed with the apple sauce, the stuff actually stands a better chance of making it all the way to your stomach where it can "activate" properly or whatever. Whereas if you were to just swallow it normally, it would mostly just coat the back of your tongue and throat and eventually absorb into your system that way, and not really do its job. Like with painkillers they're going to end up in your bloodstream one way or another, but with this stuff they're having you take, I figure it's meant to go to work directly on the contents of your stomach.
But I don't actually know.