This official statement clarifies everything:
http://counterparty.io/news/symbiont-and-counterparty/
[…]
As several realities became abundantly clear to us on both the regulatory and technical fronts, we developed technology based on Counterparty, but which differs from Counterparty itself in a number of key ways, being optimized a private network with known participants. This technology (layered on the Bitcoin blockchain) was at the root of the demonstration we provided.
[…]
Counterparty is a core part of the Symbiont “tech stack”, with entirely complementary technology to the other systems we are developing. In cases where public network on public blockchain (Bitcoin) solutions are most appropriate, Counterparty is the prime tool in our toolbelt.
Effectively, nothing has changed with respect to our enthusiasm for the potential of Counterparty, and permissioned ledgers will augment Symbiont’s platform offerings, not compete with the many market uses for Counterparty. We will continue to support the Counterparty ecosystem by providing development resources[,]