Yes, there is an alternate boarding area. You wait in line until the point where they are assigning rooms for the preshow. At that point, they pull out wheelchair users so you will go into the first preshow room beyond the CM who stands at the podium directing people where to go.
Be sure to ask for the alternate boarding area. Here is a picture of it.
and here is the description from my photo page:
The regular boarding area involves a step down to the seat of the car. There is an alternate boarding area where you can make a level transfer from the wheelchair parked right next to the ride car. A bit like transferring to a bathtub (a high bathtub).
Getting in and out of the car at that point is a bit like getting in/out of a bathtub with a high side. In the picture, you can see that the side of the ride car is about at the height of the CM's knees, so a pretty high step. The top of it was roughly level with the seat of my daughter's wheelchair - about 22-24 inches high.
You need to either sit on the side and swing the legs over and then sort of 'shimmy' down or step over the side (which you can see from the picture is rather high). Getting in and out is not graceful (at least for us) and I am glad that not too many people are able to see us. Maybe not graceful or really easy, but it works.
People with wheelchairs need to come back to that area to get off since the wheelchair will be left there. People without wheelchairs can get off at the 'regular' spot.
To get to that spot involves asking the CM at the time that you are asked how many are in your party. The seat belt check point is at a higher part of the track, so getting there involves a trip up a set of stairs with a CM (one flight of stairs, a landing, then another flight of stairs). There is also a small elevator big enough to carry one wheelchair or
ECV. When getting off the ride, you have to reverse those steps to get to the exit.
I agree with you too...the older and bigger my DD gets....graceful is not EVEN in our vocabulary! 
