That seems fair. You have to do that otherwise the dirt will keep it from burning right?
Etexas is right about the dirt in the pile. Get your dozer man to understand that you dont mind the extra time it takes to roll the dirt out. But even rolling out the extra dirt I think your initial estimates are extremely high. I do land clearing in south Ms. Rarely will an acre of extremely thick material exceed 7-800 dollars when just pushing into burn piles. Usually works out in the 450-600 an acre range.
Why not look at your local rental yards, see what kind of equipment they have and get a price and do it yourself? Knock it all down, push it in a pile for disposal at your leasure. Backdrag to suit or A pickup truck dragging a chainlink fence gate / whatnot will do a lot of leveling ....or a quad/atv.
Post up some pics of the 3 acres.