Having a rotated, portrait mode desktop with Sun Ray is something that has been frequently asked for. With the Xnewt X Server for Sun Ray and its support for the RandR (Resize and Rotate) extension this is now possible.
To test this, I installed the latest Sun Ray Software 5 EA 2. Next to a fairly standard installation and configuration I made sure that for every session (both for pseudo tokens and normal tokens) xrandr is called. This utility takes several options. In my case I used it as:
/usr/X11/bin/xrandr -o left
Not having a fancy portrait mode monitor at hand, I decided to just turn my monitor 90 degrees. What you can see in the very short (1m20s) video below is that both the login screen and also the desktop itself shows up in portrait mode. This is of course exactly what I want! All the information displayed from the firmware itself, is of course still in landscape mode. As far as I know this is something that can not be changed right now.
Have fun, Rene.

