There is no way I know of to protect a map such that the MPQ file is unreadable. Warcraft III must be able to read the MPQ file in order to play the map, and consequently, an MPQ editor will be able to as well. You can obfuscate the map file such that the world editor cannot open it, however.
I remember reading something a while back about there being a value in the header of MPQ files which stores how many files there are in the archive, which only MPQ editors use.
I do know this - xenforo dropped the ball by not keeping the vbulletin reputation comments as a feature. The loss of the Reputation comments data when we switched to Xenforo really was the death knell for the site when it came to all the users that left. I know I missed it so much and I got way less interested in the site when that feature was gone and I run the site.
I'm on a page about incorrect corrections, and spent the better part of like two hours trying to get someone to understand that -5^2 = -25, not 25, and then that post had comments get reposted because that group is self sustaining, and that person was in turn trying to explain what I just explained to them. And I'm taking that as a victory