That's true as well, but who says that one has to merge with the KH in question in order to have it destroyed.
Ansem the Wise tried to undo the KH in KH 2 on his own with his encoder, but it didn't work for several reasons, one of them may have been actually because Xemnas was still existing.
What is often overlooked is that these Xehanort incarnations actually made/build those KHs with material provided by their underlings.
The KH in KH 1 was built by Ansem SoD with world hearts provided by his Heartless armies while the one in KH 2 was built by Xemnas with human hearts provided by "his" Keyblade Wielders Roxas and Xion (and later Sora).
We know nothing about the hows and whys, but I imagine that if these two build those KHs they are also somewhat tied to them, and thus the artificial (thus not natural) KH they created cannot be fully undone unless they themselves are defeated.
Defeating Ansem in KH 1 probably broke the hold he had on the captive world hearts inside "his" KH, just like defeating an Emblem breaks the hold on the hearts they have stolen and purifies them.