Unless there are molded models of the ethercons that I don't know about wouldn't it be easier to just remove the ethercon connector? Also I seem to remember that the CAT5e and CAT6 ethercons are not compatible with each other or something weird like that. Keep that in mind.
Depends on the flavor of ethercon end. Some brands are not user serviceable and are effectively molded together like you say (And in many cases without any shield bonding despite being listed as cat6!). Also, many ethercon connectors require you to snap the locking tab off the RJ45 end, so simply removing the ethercon shell would result in a very unreliable connection at one end. Neutrik also notes that some of their connectors are not compatible with cat6 panel connectors, so I'm not sure if it's some physical aspect of the connectors themselves or the difference in cat5/6 protocols and other ethernet standards (PoE, etc).
It's also worth nothing that a lot of the d-series panel connectors have standard RJ45 outlets on the back side, so if your non-ethercon equipment usually lives in or near a rackable space you could just mount one to a punchout plate and run a standard ethernet cable from there.