I observed this suboptimal setup for all these four years before finally speaking up today. I politely pointed out the problem, explaining that while it likely wouldn't be a big deal for a few beans to get mixed into the meat, vegetarians generally have a bigger problem with meat getting into their food. The gentleman behind the counter (who I believe is the manager, which is part of why I waited until a time he was serving me before asking) immediately agreed to switch the positions of the bins beginning on Monday.
Wow. I thanked him and made sure to leave a tip. I wish I wouldn't be so shy about speaking up about these things.