Watch folder that only processes one item at a time?
Try Hazel from https://www.noodlesoft.com

I haven’t had any processes that run that long, but in my experience Hazel always seems to operate sequentially on files, and won’t start a new process until the old one is done. 

It’s an invaluable Mac app, IMO. I use it exclusively instead of
Folder Actions. It’s a paid app, but there is a free, full-featured demo available. The developer is also very helpful and the app is well-maintained. Highly recommended. 

I think your only other alternative is a lock file, which is awkward, as you mentioned.