Thanks @salias for noting this. I have edited the original tutorial to note this for future readers (but I decided to keep the link to q2-ghosttree for posterity, in case this inspires anyone to come up with an alternative solution). My how much has changed in the past 6 years since when this tutorial was written!
I am not aware of an alternative method at the moment. But hopefully if other QIIME 2 forum members know of one they can suggest a solution.