Read the Tarasov article. The organ was used as a continuo in any large-scale music from the Baroque where it was available. Most of Bach's cantatas would have been written to be played that way.

As Tarasov explains (or assumes), the choir sang to the organ all the time, so they used the organ's pitch, hence the name "Chorton" for whatever pitch standard the organ was tuned to. The orchestra might play in places where there was no organ a lot of the time, hence used their own pitch standard, "Kammerton". The difference between the two (in a single musical establishment in a single place) could be as much as a minor third, and was not the same on every occasion when Bach was writing a cantata. So some of these early cantatas are scored with the orchestra in one key and the choir and organ in another.