Yes he has. (More than that, if you take into account what 'The Moment' did in the Time War) Typically the Daleks and usually after giving the species a chance.

But with the Silents, he ENJOYED it. With the Silents, HE didn't do it: he hypnotized the humans into doing it FOR him. So I stand by my reasoning that the issue with the Silents is far more horrific than anything else he has done.