Yes. That certainly would have been an issue if I were doing the testing on an XHTML 1.1 page. In fact, however, I'm doing it on a kind of "gateway" page that gives access to more than one distance-learning courses, only one of which (a Calculus course) needs the full MathML capability. So I serve the gateway page and all the non-Calculus course pages as XHTML 1.0 Transitional.
If someone using IE6 or IE7 then wants to access the Calculus course, I additionally check for the presence of DesignScience's free MathPlayer plugin (http://www.dessci.com/en/products/mathplayer/). When running this plugin on IE it has the effect of overwriting the DOCTYPE of the XHTML 1.1 pages, making their content available as text/ html. Ed Martin