‘transform’ alters the orientation of the entire element you declare it on, not the text content inside it. It's more like IE's ‘matrix’ property than ‘writing-mode’.
Crucially, transforming an element doesn't change how its content size is calculated (or how its parent's layout is affected by that size). CSS's algorithms for vertical and horizontal sizing are different and difficult enough to get right to being with; there's no real consistent way they could accomodate content with arbitrary rotation. So ‘transform’ is like using ‘position: relative’: it changes where the content is rendered, but not anything to do with layout size.
So if you want to include one in a table you'll need to set the cell's ‘height’ explicitly to accomodate the expected rotated ‘width’. If you don't know that in advance you could potentially hack it up with JavaScript, perhaps.
FWIW: for me on Fx3.1b3 the span is also rotated like the others. However on Windows with its horizontal-only anti-aliasing (ClearType) the rendering doesn't look great... a well-rendered image could come out considerably better.