Depending on how much effort you have spent integrating wth Gazebo, I would
suggest considering using OpenRAVE for this sort of work. We use if for a
number of simulation and planning roles including a case very similar to
what you describe - we have run a robot with "virtual" obstacles that only
exist in in the simulation environment, so the robot considers obstacles
gathered from real data from its sensors and also an obstacle that only
existed in the simulation. There are nodes/plugins that provide this
functionality in the openrave_planning stack.

We overcame synchronisation problems between real-time on the robot and
simulation time by simplifying the  simulation as required to get it to run
close-to real time. For short-term experiments it ran fine, there are
probably better ways to do that though.
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