I like to think of them as purely moral choices, not at ALL for practicality.
In the beginning of R2, Kallen asked if she was geassed into obeying Zero, or something to that effect. Lelouch makes it clear that she followed under her own will, which presumably, he wanted for all of the Black Knights.
Note that he only ordered "Obey Me!!!" after the Black Knights betray him*, leaving him with no troops to command.
The others I see as lack of choices. For example, he didn't geass Suzaku the moment he realized he was working for the enemy (he could have very well said "Follow Zero" at that point on, and C.C. even chastises him for not doing it) but he only geasses him in a very precarious situation (when both of them were about to get killed).
*EDIT: Actually, there's another reason: (Lelouch thinks) NUNNALY's DEAD!. Remember he did everything for Nunnaly. With Nunnaly, Shirley, Rolo, and the Black knights gone, he has nothing left basically. So this point is pretty much a "Well, Fuck My Moral Compass", And does things more pragmatically.