Droids in the Star Wars universe are slaves (as are the Clones).

So they will politely take whatever is thrown at them.

If Dooku had ordered them to try their best to kill Grevious they would do that politely too (just as the Clones do when ordered to kill their former Generals).

Neither army is evil as such as they lack free will.

The sequel saga (which George says will never happen) should have dealt with this issue.

Obi-Wan does postulate the interesting notion of, "Well, if droids could think, none of us would be here".

The saga has two droids as main characters who constantly use their own initiative, it's not a huge leap to imagine a nuGalactica style droid/clone epiphanic revolt.

Though this thread isn't really the place for talking about such things as none of this has much of a bearing on ROTJ or ESB (other than altering the stupid comedy droid torture scene).