No, it shouldn't be done that way. Doing it that way creates duplicate profiles. Duplicate profiles create somehing in the software background called a redirect. Redirects are not healthy for software, it causes extra steps in the computing process. Extra steps take time, time is cost, like one domino pushing the next.
I understand the problem you face. However, it's like there's already a library and you have come upon a newer collection of the same books that are already in the library. The librarian must replace each individual volume one by one, as painstaking as that task is, making sure each volume is catalogued and nothing gets misplaced. The librarian wishes the new books would have been provided in the first place, however, that didn't happen. So the librarian must do it the hard way, even if it takes him/her a great deal of time.
I don't mean to make your chore seem impossible, but with so many profiles, you are most likely to have a near relative come along and help to sort out all of these profiles. At least you already have the profiles on the Wikitree.