This has been a huge issue so I thought I would post it here letting you all know about it.
Kenjar has posted his Keybinding application over on STLA, check it out here: http://stlegacyalliance.com/showthread.php?t=179
This should help relieve A LOT of the trouble associated with changing the control keys.
PS: If you need support or other needs you can eithier post on the thread listed above or give him a PM.
PSS: Kenjar's blog is located at http://stlegacy.com