You can do this with the config option "merge.ff = false". Set it once and you're done. The "Properties" view in the "Git Repository" perspective provides a simple gui for showing and editing your configuration settings at each level. The only caveat is that you must restart eclipse after editing the configuration for jgit and/or egit to pick up the change. At least that's what I found in my tests.

Using the Git configuration mechanism seems cleaner than adding an option to the egit gui, which has plenty to do already.