In theory, Perl 6/Parrot would make a good basis for a new Bio-project, bringing the best of OO, functional, and perhaps even parallelism to the table to provide for a clean and efficient solution. But even then, it would be a surprise to me if anything more was done than just to re-implement the existing Bio-Perl interfaces as quickly and directly as possible, without spending any time exploring how the new language and facilities it provides could be best utilised.
BioPerl has already started its way to Moose (BioMoose) as a first step towards BioPerl6. But after reading the seminal posts on the BioPerl mailing list, I'm afraid that you are right in your predictions. Sadly, I don't expect more than a porting re-implementation