Sometimes it is easy to see why there are disputes about parentage a few hundred years ago.
In more recent years it should be easier - if someone has made an honest mistake, and another person has found out more up to date information (backed up by good sources). Collaboration, after all, is one of the key mottos of Wikitree.
Is your great grandfather's profile open? If so, you can add the disputed information (bearing in mind that the other person presumably thinks that their information is correct).
If not, and the profile manager is resistant to your ideas, I can only suggest that you add your 2G grandparents and their ancestors separately, complete with sources. Then add your greatgrandparent as a child.
I think that they would then show as an alternate set of parents, which may be the best solution, if not the one that you feel is correct.
Someone who has been here longer may have another suggestion.
Margaret