I think it would be better if we split the documentation for Pluto 1.x and 2.x instead of this mixture within one site, similar to what we're in the process of doing for Jetspeed 2.1.x and 2.2.x
Furthermore, as I have proposed elsewhere, I think we should consider moving the documentation outside of the main release related trunk and keep it separately like under /portals/site/pluto/pluto-1 and /portals/site/pluto/pluto-2.
Anyway, besides that point, I think you're raising a valid technical concern here.
It will indeed be a problem to have both the old and new pluginGroup defined with the current plugin prefix which is the same for both.
The only way to solve that is changing the maven plugin prefix to like pluto2 for Pluto 2.0.
Good catch, this late in the game (we're planning to start the release process for Pluto any time now)
I'll create a new JIRA issue for this and fix it which only requires a simple configuration change in the plugin definition.