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Two options (off the top of my head):

don't have one sourced when you're building the other (ie: don't have source /some/path/to/catkin_ws/devel/setup.bash in your .bashrc (or similar file))
use catkin_tools and initialise the configuration of the respective workspaces with the --extend option to explicitly extend (or really: overlay) /opt/ros/kinetic

Two options (off the top of my head):

don't have one sourced when you're building the other (ie: don't have source /some/path/to/catkin_ws/devel/setup.bash in your .bashrc (or similar file))
use catkin_tools and initialise the configuration of the respective workspaces with the --extend option to explicitly extend (or really: overlay) /opt/ros/kinetic

Edit: perhaps three: sourceing a setup file should override whatever vars are already present in your environment, so if you'd source /opt/ros/kinetic/setup.bash before building either workspace it should (implicitly) extend /opt/ros/kinetic. I'm not sure how reliable that is though, so personally I would probably go for option 1 or 2 (actually I do both: I have 50 workspaces and none of those are sourced automatically).