Being in Retail management (though not the food business) as well, I really think that this is probably par for the course. He asked you for your ID for the booze (whether or not he was required by law is up to your state, I don't know, but I don't think it's unreasonable); now, you want to write a check, something that every place is going to want to see ID's for. Should he have taken care of everything at once? Maybe, but I doubt it. The only thing that I can think is that if he waited until the end of the purchase to ring up the booze, and he KNEW that you were writing a check, then he could have just asked for it, and not given it back until he was done. Otherwise, I don't know what else he could have done.
The question I'd be asking is why I'm writing checks still. LOL, not to be a jerk, but debit card, man!! LOL, I don't know, I try to convert my parents to it all the time, too and they refuse, as well. To each their own, but that's part of the inconvenience of checks.