Hildon-input-method can be disabled.

There is something like "/usr/bin/hildon-input-method &" at the end of the "/usr/bin/start-hildon" script, just remove that line.

How about splitting the start-hildon into pieces like nokia did? (/etc/osso-af-init).
Then there could be separate files for each part of the hildon. For example, if there's a separate file for matchbox-window-manager startup, movable dialogs could be set without the risk of messing up anything else.