Was there something specific it the data model that made the versioning hard to write? Or was it that, for this to work across the board, the entire model had to be versioned?
It sounds that SQL itself wasn't the problem. Were you looking for versioning alternatives in SQL that weren't up to par?
SQL was a solution more than a problem; we were just hoping for a simpler or more elegant solution.
For example, it's possible that logging all data model changes to a text file would have given us the persistence we were looking for without bridging all our data to SQL. Cutting out SQL from our production set-up would have been an inherent win -- one less process to manage, one less black-box source of complexity, etc.
It sounds that SQL itself wasn't the problem. Were you looking for versioning alternatives in SQL that weren't up to par?