I closed a hog lagoon 20 some odd years ago as well. Not only NRCS but the DNR was involved as well. 
If I recall the payment was for the solid portion of the lagoon. Besides the guy that pumped it a good dozer operator is needed as well. As the lagoon is pumped a dozer continually pushed in the sludge into a smaller pool in the center of the lagoon. 
Long story short, The government paid about $50k to close the lagoon. The pumper cost $20k and the dozer was $20k. I ended up making about $10k plus the value of the manure, which was substantial.