To add to what @JamesSekcienski said, the SIS is considered the authoritative source of information and contains data that doesn't get put into Canvas. If you have a good working relationship with the people who control the SIS, then that's where the information should come from. Thankfully, I need read access to our SIS so that I can get the SIS imports prepared for Canvas. Some institutions have completely separate departments that don't play well together, so people think it's easier to get the data from Canvas -- especially if you have CD2 -- than from the SIS.
If getting data from the SIS department requires donating a kidney or thirty-two forms signed in triplicate, then I have an idea that might work.
I'll call the idea a longshot and don't hold out hope, but I'll throw it out there. If all of the instructors are created with the same role in Canvas, but the secondary instructors get added later, then you could use the canvas_enrollments.created_at field to determine which enrollment got added first.
For example, many of our health professions courses have multiple instructors within Canvas. As James suggested, the primary one is doing most of the work and you could use the canvas__enrollments.total_activity_time or .last_activity_at files to pick that out. For us, most of the others don't go in at all, but that's not guaranteed.
But for us, the primary instructor is added automatically by my code that with the same SIS import that creates the course and adds any already-enrolled students. The secondary instructors aren't listed in our SIS as instructors, they are just the other instructors who happen to teach the course. Since they are manually added later, we could use the created_at field to determine the primary one.
All of that assumes that the original primary instructor is still the current instructor. We sometimes change instructors and move sections around. In that case, we would have to rely on the SIS.
I concur about having separate databases not being ideal. Our SIS uses Informix; our CD2 uses MySQL.