They're not segregating them the entire time, so it doesn't mean they'll never learn to resolve their differences. Lunchtime is a difficult time supervision-wise - teachers are entitled to their lunch break, and so most schools rely on employing lunchtime supervisors, and the more you have, the more it costs. So anything that makes the supervision easier will help. Plenty of space doesn't always help - it makes supervision harder.
The individuals causing trouble missing the lunchbreak every day is not a practical solution. They still need to be supervised, so you'd then be using someone on just those children. Also, they're often the children who most need to run off some steam at lunchtime so that they can settle in the afternoon.
If it had always been the system that the teacher would tell the kids each day who was on first and second lunch, there would probably be no complaint - they'd have accepted the system.
Sure, they'll complain about it, just as they'll complain that they had to work with Jonny in science today, and that it wasn't their group's turn for cooking.
If your child is really struggling with the system for some reason, then have a quiet word with the teacher. It may be that there's a good reason to try and avoid swapping your child about, but I don't think it's a reason to stop the system altogether.