We arrived the night before our adventure, checked into the Wort, and did the School of Science excursion the next morning. It did not really seem like 5am, because we were on east coast time, but I would have gotten up earlier for it. For us it was really good, for we had never been in this part of the country and it really gave us a good taste for what we were in for with Disney. We had the guide to ourselves and he built the tour around what we wanted to see. We had a great hike near Jenny lake (different from Disney's). Saw a Bison make a standing Jump over a split rail fence (doesn't sound like much but wait until you see how large they are, and you will understand the awe factor). Saw a Antelope stalking and chasing a coyote (we think she had a fawn nearby). Every time we saw a interesting wildlife event, we were able to get the excursion bus fairly close and sit and watch it, which was a little better then Disney could do with the big bus. The wildlife pictures we got were great. The guide (which is a biologist) had some teaching aids (skulls, pelts etc..) and was great with the kids, 10 and 12 year olds. After lunch with the guide, we had the afternoon to explore Jackson before the welcome dinner with Disney. There would have been plenty of time for a nap. In my opinion Jackson is not very big and you will get enough of it with Disney's Free afternoon and the afternoon after the science excursion.
I had the same feeling as you, knowing how much we had spent to get there and not wanting to waste any time and we were real hesitant to spend the extra money, but I would say it was well worth it and I would do it again.