We have had a number of questions regarding the diagram comparison support in EMF Compare 2. This is something that was (somewhat) provided with EMF Compare 1.3, but that we have yet to port to the new version of the APIs.
Well, the work is ongoing and preliminary support for diagram comparison is available in the current integration builds. The port was done in the context of the modeling platform working group and is mainly targetting Papyrus, though ecoretools diagrams (and plain GMF diagrams) should also be supported.
We have not fully settled down on how to represent deletions on a diagram, but this otherwise begins to take form :