I'm with them. If you're regular enough that they know who you are, I think the odds are that if you go and explain what the issue means to you in as neutral a manner as possible, they are likely to find some way to accommodate you.

This doesn't have to be done in a way that includes "apologizing for your allergies" -- e.g. "I'm sorry that I have this allergic reaction," but expressing regret that it's come to this -- i.e. "I'm sorry about this but if there's going to be smoking near the entrance of the cafe, I'm going to have to take my friends to another cafe, and I'd hate to do that because I like this place so much -- is there anything we can do?"