I'm a little late to this discussion, but maybe I can bring the perspective 
of a pathologist it.

The pathologist is looking, not for ganglion cells, but for the LACK of 
ganglion cells in portions of bowel biopsied or resected for colonic 
aganglionosis (Hirschsprung's disease). Obviously it's difficult to prove a 
negative.

Usually H & E will do the job. The non-specific esterase technique one of you 
described (with naphthyl acetate as the substrate) is extremely rapid, and 
suitable for use at frozen section during surgery. It has the disadvantage 
that it also demonstrates esterase activity in epithelial cells and 
macrophages. Sometimes the distinctive nuclear morphology of ganglion cells 
gets around this problem, but it's difficult to identify ganglion cells in 
the submucosal (Meissner's) plexus. I have used this technique successfully 
during surgery - a LONG time ago.

As far as I know, more specific techniques for cholinesterase are too slow 
for frozen section use.

Bob Richmond
Samurai Pathologist
Knoxville TN