I would not let a bike into a restaurant either - no offence but it is a matter of principle. If you let a bike in, then why not a moped or motorbike? You have to draw a line somewhere. Also they wouldn't want a little kid to squeeze by you and perhaps cut their leg on your cogs. you probably maintain your bike well, but as we all know there are some bikes with jagged edges on and rust. Having said that, they should let you use the drive-through. Some don't even let motorbikes through the drive-through, don't know why as you pay before you get your food. It is pure discrimination.
With regards to "policies" - this is a statement that is used far too much. if someone tells you it's against their policy then they should know where that policy is and be able to tell you what page it is on. policies have to be drawn up, circulated to board members and executives, then signed off. Asking the manager and then quoting his reply is not a "policy".