The difference is Lelouch wasn't ordering Rolo to do anything (i.e. "Good job" does not really translate to a command). I don't think Rolo's looking him directly in the eye when he starts suggesting the massacre of the cult. The question Lelouch posed to Euphie was structured accidentally as a command. Sort of like "even if I ordered you to kill all Japanese people*Geass kicks in*
(no subject)