If I were the customer in front of you, I'd be tempted to pull out my cell phone, dial the office number, and see whether they put the first telephone call on hold to talk to me. If they did, I'd try to go ahead with the check-in, or give them my credit card number to pay for the day's bill, or what-have you.
But you can't do that, though you might be able to wink and say "sorry, but we've been told to always deal with telephone calls, even if we're already talking to someone." And you can definitely say "I'm sorry, that's the policy I've been given. If you'd like to fill out this comment card, maybe they'll change the policy."