No one has ever been banned for using Companion Remote Desktop. The SWTOR EULA prevents the player from doing things that are illegal i.e. botting, cheating, macroing. Companion Remote Desktop does not give the player any of these abilities.
Lots of people get freaked out about the Third Party Software clause in the EULA saying "CRD is 3rd party software, you can't use it!". News flash, Windows is 3rd party software, Ventrilo is 3rd party software, DirectX is 3rd party software, your Logitech G15 keyboard driver is 3rd party software. This software is all ok because it doesn't break any rules of the EULA. Similarly, CRD does not break any rules of the EULA.
Regards,
Zach
Hypercane Studios