Hi!
Using custom HTTP headers would, of course, complicate calls for the tool authors (i.e., myself). $.ajax instead of $.get and all that. I would be less inclined to change to that.
Yes, if you're using browser, you probably can't change user agent. In that case I guess we need either X-Analytics or put it in the query. Or maybe Referer header would be fine then - it is also recorded. If Referer is distinct enough it can be used then.