From DerekGary in the forums:
I ran into an issue upgrading SCCM 2012 to sp1 where the prereq check failed due to Active Replicas in place. This happened despite following the Technet article on completely removing the replicas (you have to remove all subscriptions and publications, and delete the databases). Though I followed these steps completely, the prereq check returned the same error.
To resolve this error, I had to go into SQL Management Studio, and Disable Distribution through the Replication node. When this completed, I reran the prereq check successfully and can now upgrade to sp1.
Original post: SCCM 2012 sp1 Upgrade – Active Replica Error (solved)
Sadly, there are a lot of post upgrade issues, errors, and bugs filtering in. We need to keep track of all of these. If you experience a problem with the SP1 upgrade, let us know so everyone will know.