Circular dependency in schema or boolean with CHECK?
Having the origin_remote column in the repositories table allows for an intrinsic consistency, even without check, and you'll keep this consistency when changing DBMS and, more importantly, in the application code.

This also allows for a single query when you want to change the origin of a repository, while having your is_origin boolean would imply two queries which would have to be wrapped in a transaction.

In this specific case I'm of the opinion you should really use the standard relational link from repositories to origin_remote_id. The need to use alter table is just as a minor inconvenience.