My IT/network guys have told me that every time AE sniffs at the watch folder, it causes some slowdown of the network
...which in turn probably means that your network setup sucks in the first place. No offense, but you're probably looking to solve the problem on the wrong end. Beef up your servers, create a separate subnet/ sub-domain with its own set of IPs, optimize the mapping/ routing to avoid network collisions, map the AE render folder to its own drive on the server and allocate proper user resources. I mean, FCP dropping frames when someoen else accesses the server is a clear sign of network collisions because everything is handled through the same conenctions, which is just not smart. How do you get anything done at all? Saving a simple graphic or text document to this setup would cause issues....
Yes indeed our network DOES suck bigtime - despite having hundreds of terabytes of (supposedly very fast) storage and a fibrechannel card in every Mac, plus full-time IT support staff, it is unreliable and (relatively) slow. One of those variables is apparently not up to the task. So I have to work with what I've got, unfortunately.
But, on a more positive note, someone on another forum suggested using an automated script to click on the 'pause' button in the watch folder progress window every x seconds. Far from an ideal situation, but until the deficient part of our network is improved, it'll probably have to do for now.