It is possible to add a command line in the AviSynth script to rotate the picture 90 degrees, but you are equally likely to stretch the picture and distort it doing this within AVStoDVD.
If you want to try it, import your video with the green + sign in the main window of AVStoDVD, then just under the green + sign, click on the gear icon to View/Edit Title Settings. This gives you a pop up window, so move to the AviSynth tab. Take the check mark out of the Automatic box and insert this line:
Video = Video.TurnLeft
You'll notice that there is a space on each side of the = symbol.
To preview the effect, click on the gear icon at the bottom left of the screen in the AviSynth tab.