I don’t think this is weird at all. In fact, I think you are really smart to see how the different actors work with each other. Run it efficiently, and respectfully, and you are fine.
I would schedule it thusly: (put whatever times you like, obviously)
Callback Appointment Times:
9:00am - Jill and Bill
9:15am - John
9:30am - Jane
At 9:00am, Jill can read with Bill.
At 9:15am, ask Jill to stay in the room and ask Bill to wait outside. Call in John to read with Jill.
At 9:30am, release Jill, and ask John to wait outside. Call in both Jane and Bill to read together.
At 9:45am, release Bill, ask Jane to stay in the room, and call in John to read with Jane.
If you do it this way, each person gets to read with each partner, but you are not wasting any one person’s time by making them wait the whole time. Sometimes this can’t be avoided, and people just have to wait, but it’s respectful to avoid if you can.
I also like this because it gives each set of partners privacy while they are reading. I think you’ll get a better, less self-conscious reading if all four people aren’t watching each other the whole time.
Lastly, I’ll encourage you to take your time to get what you need out of the audition. Don’t feel rushed. Give the different pairs a few notes, and let them try the scene a couple of times so you can really see how they look and work together.
Let me know if you have any other questions, and good luck! I hope you feel great about your cast after these callbacks.