The symptoms described in the ticket do not match yours.
You wrote that you're getting the error even when running
makemigrations, whereas the reporter of that ticket wrote that
makemigrations succeeds, but a subsequent migrate fails.
From what you described, it seems like your project tries to perform a
database query on startup, which obviously will not work before you
actually create the database with an up-to-date schema. It's
impossible to tell with certainty without seeing the full traceback or
any code, but it looks like you are trying to fetch a Site object from
the database on startup (as in, one of your applications makes queries
on import time). This is simply not supported, because such an
operation does not make sense, when you think about it. (There's a
chicken-and-egg problem in this scenario.)
All in all, from your description is seems to me that there is nothing
Django can do about the issue, but you'll have to provide more
information in order for us to help you resolve the problem.
Cheers,
Michal