whats the difference between morale and command stars?

[Togakure]

I know that 2 stars of the general give +1 valor to the units ....

Yes, and each +1 valor gives a unit +1 Attack, +1 Defense, and +2 morale. My impression has always been that the additional bonuses/penalties affecting a general as a result of virtues or vices are added on top of this basic mechanic.

I still have Yaz' Units Master Tools, which confirms the Attack, Defense, and Morale bonuses per Valor point.

Regarding the original question, assuming no other vice/virtue effects, yes, the net effect is no morale bonus for the stack (6-stars = +3 valor = +6 morale to each unit; -6 vice penalty negates morale bonus; Attack/Defense bonuses from 6 stars unaffected).