(i asked some advice on the jboss developers mailing list)
my first thought is that we should have 2 service archives, both with their own database tables. i think merging the database will lead to maintenance and integration nightmares.
One plain jBPM/jPDL service archive and one BPEL service archive. We should also add that these service archives check if the database is already present. if not, the service archives should then create the tables automatically.
One option is that you create a separate database for each of these. But another option is that you change the prefix for the BPEL tables. That would allow people to use jPDL and BPEL in the same database.
There is a parallel discussion on this subject which focuses on the impact on the AS/testsuite here.
I agree merging the database would be problematic, particularly because BPEL does not use the latest version of jBPM due to time constraints (it follows closely, tough). Further, users can still deploy jPDL processes to the BPEL database if their processes are compatible with the older jBPM version.
I'll change the BPEL prefixes in the next release.