In many cases for early Acadians, it wasn't clear what, if any standard spelling was used, so it made it difficult to follow the "use their spelling" rule you point out. For that reason, we came up with this list of standardized spellings.
The problems we were trying to solve is how to deal with names that have many spelling variations today and back then, such as mine. Many of our ancestors did not write, so the spelling in the documents was at the whim of priests, census takers, etc.
Now, the question of when to switch from an earlier standardized spelling to contemporary spelling is a good one. My feeling on this is when we start seeing consistancy in the docuements.
Back to the Sire/Cyr case, are the early documents consistent with the Sire spelling? If so, that could be a good enough reason to switch to Sire as the standardized spelling.