How do I prevent iTunes from syncing down Voice Memos from my iPhone?
Currently, there doesn't seem to be a way to prevent iTunes from pulling in the voice memos. The closest I've been able to figure would be to have a script or launchd item that simply removes anything that it sees. Preferable copying them to another directory for storage. 

Update: October, 2017

I've switched to using Just Press Record which is dedicated to voice memos. It's fast to start and also creates transcripts. They're pretty good most of the time, but sometimes they get pretty far off. It's a nice feature, regardless.

The app costs a few bucks, but it's well worth it. (And, I like to support developers so they can keep working on software I like.)