Kostya,
After about 2 years of happily using Aquamail, I've realized that I have never used the button "delete". Rather, I always use "Delete now/Delete immediately".
I understand, that I am not the statistically "average" user, but I suspect there might be a few that do it the same way.
So, I hope it wouldn't be very difficult to implement yet another configuration option for the "Delete" button (in all its "incarnations": message view, list view, notifications, ...): "Delete now" or "move to `deleted' folder". And of course, keeping the latter (the present behavior) as the default option. Since "delete now" has a confirmation anyway, I don't think this would confuse people or would lead to accidental message erasure. (Well, you can put a warning sign next to that option in settings.)
BTW, using this opportunity, there are two different menu items for "Delete now" function: "Delete now" in the message view, and "Delete immediately" in the [message] list view. I am not sure which one is better, but just pick one for consistency.
Thank you for reading this!