Hi William,
The new rosdep spec restricts each rule to specify one package manager:
http://www.ros.org/reps/rep-0111.html#single-package-manager-per-rule
As I understand that restriction, you'd have to switch the appropriate rosdep.yaml to pull graphviz via brew instead of macports. I think that the rationale is that we want to minimize sources of variation in the underlying system.
brian.