Peter, this is very confusing, and somewhat contradictory.
I sincerely doubt that the large majority of KM users would want to cause the KM "Copy" Action, or the "Type a Keystroke of ⌘C" to ALWAYS fail.
I'm going to guess that the "Copy" Action, or some type of Clipboard processing is one of the most used functions of KM.
What does this mean? Are you referring to setting of KM Preferences by command line?
If that be the case, then you should provide a BIG WARNING at the top of that section of the KM Wiki that clearly states the danger of setting these preferences.
All of this points to the need to provide for setting of ALL KM Preferences via UI in the KM Preferences Window. There you could control and ensure valid settings, as well as provide a popup warning if the user is making a change that can have a major impact.
Why not put all of the preferences you currently provide via command line in the Preferences UI, in an "Advanced" tab that hides it from the user unless the user specifically clicks on that tab.