I made the following web.xml in my war – and it works directly in Pluto 1.1 and Pluto 1.0 environments – at least it works in Sakai 2.4 (Pluto 1.1) and uPortal 2.5 (Pluto 1.0).
I initialize the servlet with both sets of parameters (thankfully no overlap in names) and then provide two servlet mappings.
It seems deceptively simple. Of course this is doing wildly different things at run-time – but depending on whichever Pluto you are running – it sees what it wants to see and ignores the rest.
Comments/feedback please.

<?xml version=”1.0″?>
<!DOCTYPE web-app PUBLIC “-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN”