In some other scripts, such as the Arabic script, visual encoding is not an option, so one should expect increasing support for logical encoding. The advantages of the logical method as a long run solution are evident. Unfortunately, there are many users with older browsers who cannot render these pages correctly. In order to accomodate both, but in the same time give a good service to users of BiDi browsers I would suggest writing two versions of the website. The logical version should be considered as the primary one, using efficient fast loading pages, styled with style sheets, and the visual one, as a transitional measure, for backward compatibility.
Many websites have only a visual version.
It wouldn't cost you much more, as the text is originally encoded logically anyway. An article by Lior Eilam reporting on a survey of usage of BiDi browsers, among other things.