MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Just thinking out loud: How about using captive magnets? It'd make the print a little bit trickier, but the end result would be a lot safer.
A drawback would be that the magnets won't touch anymore, thus reducing the rigidity of the magnetic connections.