As occasionally happens, I give up and move onto the next bug hoping that the next bug will be easier to fix and/or give me some insight into the previous bug. As it turned out, I moved onto bug #409793 which was a performance bug on sites like Ink Journal and Ink Tattoo Studio.
What was happening on these sites was that as more points got added to the stroke, rendering would get slower and slower (thus causing the line to lag behind the mouse cursor) because Moonlight was invalidating the entire InkPresenter canvas on each frame and so having to render the entire thing even though it was unnecessary.
To optimize this, I added a 'dirty' rectangle that kept track of the actual regions we needed to redraw. As points got added to the collection between frames, I added the bounds of the new point plus the region between the new point and the previous/next points (the 'next' point is obviously only needed if the newly added point was an insertion). The result for sites like InkJournal and InkTattooStudio was that we only invalidated the newly appended points at each frame render, vastly improving our performance which now matches Microsoft's Silverlight performance for these sites afaict.