I've always found replacing maps with someone else's to be a rather touchy subject.
Objectively, the better set of maps deserves to be on the site for any given game. Subjectively however, my opinion would depend on the quality of the maps being replaced and the difference in quality between the original and the replacement. I'll admit my reasoning is purely emotional because even though I rarely receive comments about my work, it still feels good to know they're being featured on VGMaps for everyone to see, and knowing they're considered good enough to be there. If I did a crappy or incomplete map and someone else submits a much better one, then they deserve the spot more than I do. But if you've spent hundreds of hours on a game and ended up putting together very good and exhaustive maps and they get posted on the site, it would hurt a lot for them to be replaced just because someone did an even more amazing job. It would suck to see all your hard work sort of invalidated even if visitors of the site would end up winning with better maps to see.
In short, I don't know. The original Super Mario World maps clearly aren't complete since transparencies are missing and in the case of water, that's really integral to the stage. And if the maps were really taken from an editor, it should have been the mapper's job to add in what was missing. But then again, they've been given the Map of the Month award, so JonLeung is really the one who should make the call.