On the matter of indexing, I think WikiTree has already solved the most important problem -- the file is linked to one word and a number. I don't see it would be a technical IT problem to link that one word/number to several names -- maiden name, various married names, etc.
On the matter of profiles, I think the name at top should be the name the person would have wanted to be known by. So it would be Mohammed Ali, not Cassius Clay. Under that as a separate line would be the Full Name at Birth, which would be Cassius Clay. It probably would be helpful to display, again on a separate line, the index name, which if it follows LNAB, would be Clay-####. Then there could be separate lines for aliases. The current method of trying to run as much together on one line at the top results in combinations which were never known in real life.
As we do more foreign names, this would accomodate it. I've seen formal names of Latino men in the order of (1) the given name, (2) the father's last name, followed by (3) the mother's maiden name; that order should be at the top of the profile, but it's the word in (2) that would be the indexed family name.
I lived in China as a child and was given the Chinese name of Dai Wan Kwang. That was never used legally so would only appear in my profile as a curiosity, but if it were the name I used, then the family name -- which we mean by last name at birth -- would be Dai, and that's how I ought to be indexed. I am Wan Kwang of the Dai family.
None of these are problems for the index structure which is simply family name + number. Over time, I'm sure it will be possible to tinker with the graphical user interface for the profile so it accomodates different cultures more readily.