Indeed.
The one thing about this kind of action is that whenever they come up, the reason they came up to begin with is that there is simply no better alternative, and it becomes ABSOLUTELY necessary to perform it for anything resembling a better outcome.
The main conflict then is not whether it is justified to commit a smaller evil even if it is to stop a greater evil; but whether the person who have to make the choice choose to commit it (and possibly reach a relatively better outcome), or not to commit it out of whatever his/her principles he/she held (and possibly condemning the situation to go down the unthinkably worse alternative path).
If the character wants to achieve a better outcome, and there is no other choice other than lesser evil or greater evil, then there's never really a choice; the problem is whether the strength of character exists to implement it.
This is why I ended up rooting for Lelouch's approach in the struggle rather than Suzaku's - when one factors in all the info concerning how INSANELY HOPELESS the situation is for the heroes fighting against Brittania, all the lines Lelouch crossed to overthrow Brittainia becomes logical, and necessary, whereas Suzaku's approach appears nothing more than idealism that ultimately cannot last; and as we seen towards the finale, it really didn't last.