Your local NRCS office should be able to help you with your concerns.
I have a 12" siphon pipe on a pond maybe a little larger than yours with a 150 acre watershed, and have had no problems. My ES area is 1.5 ft above the the pipe on one dam end and 1.0 ft higher on the other end. The freeboard is about 4 ft, however, I close the pipe at the end of spring and allow the elevation to rise about a foot higher for the summer drought months.