Hmm ... IIRC, the Kenwood remote is telephone upgradeable; you call them, they have you hold up the remote to the phone speaker and it might be able to be upgraded to work correctly with your DSS. Have you tried calling the support number in the manual for the remote? You may be able to avoid getting another remote altogether, if control of your DSS is your main concern.
If your wife isn't technically minded with a good memory, I don't think the SL9000 is the way to go. It works fantastic for me because I remember where all the keys are for my 6 components (I try to maintain some consistency in choosing layout; display always on the info button, menu buttons always in the same place, etc.). I can find all buttons by feel and never even look at the labels. But for someone who has to look at the labels to figure out what they do, it just doesn't work. You can use stick-ons for some, but they won't change for each component.
I do think the Marantz is worth the extra money over the Sony ... Custom labels are nice because you can deal with future components which have differently named features. The remote has a nicer shape and button layout which is good if you are a channel-flipper and like to keep the remote in hand and frequently fiddle with things. The Marantz is good enough that it can be the last remote you ever buy, if you don't need the whiz-bang customizability of a Pronto like device.