Replication Blocks Code Deployment
We are facing the same problem - DACPAC does not support replication (as of now).

What we do is - if the deployment involves/affects replicated tables then


manually drop replication. 


Script out drop and create replication using GUI or Powershell
Drop the replication

Run your DACPAC to upgrade your system
Create replication (scripted out previously) and kick off the snapshot of articles.




UPDATE :

USING GUI :



USING PowerShell :


Quickly Script Out Replication Redux - by  CHAD MILLER
Using PowerShell to Script out Replication on SQL Server 2005/SQL Server 2008 by Paul Ibison