You're completely right about the need to differentiate which version of the language particular code is in...especially in the long transition period. Perhaps <code5>...</code5>
tags (whose contents are displayed in different fonts) might be a good starting point.
And if these were used consistently then it would be a SMOP to have the monastery itself append [Perl 5] or [Perl 6] (or both) to node titles, depending on what kind of tags the node contains.
Oh, and Perl 6 is quite a bit more imminent than you think: our goal is to have a beta out this year.