From my understanding of the Conditioning, which is so rarely mentioned as to make it one of the things that is just 'assumed' in the culture in which the series takes place, the Conditioning is a means of making sure that the Conditioned Doctor would be completely incapable of harming their client/patient. The Imperial Conditioning, thus, would allow a doctor to treat the Emperor Himself, since, with the lack of technology, and the way the poisoner's art has bloomed in the Feudal System of the Dune Series, it would be horribly easy for a Doctor to kill the Emperor. His Doctor would be one of the very few people he would ever possibly be alone with.
The Conditioning seems to be a deeply ingrained restrain against the taking of a life. However, to quote the Baron Harkonnen, "As someone once said, given a big enough lever, you can move planets. And we have found the Lever for our Doctor."
One of the other themes displayed throughout the series is the dangerousness of emotion. The series isn't just about the dangerousness of revenge. It's about the dangerousness of all emotion. Including love. What allowed the Doctor Yueh to over come the conditioning was something that conflicted with it -- just as the First Duncan Idaho was able to overcome his conditioning to kill Paul and thus have his memories restored -- love. One of the themes of the Dune series is that love is the most powerful thing in the universe, and thus greatly feared, because its effects cannot always be controlled. Love, specifically Jessica's love for her Duke, has effects that last the rest of the series (and presumably, for the rest of time.)
Doctor Yueh's love for his wife was stronger than his imperial conditioning. It may have even complimented his Conditioning in some ways. If he was conditioned to do no harm, he would have not been able to do what he was doing without the conditioning being completely broken. But the words the Baron uses 'managed to subvert a doctor of the Suk School,' seems to indicate something different. A bending, not a breaking.
The Doctor did not actually kill his Clients -- presumably, the conditioning extends only to the Client/Patient. He killed Mapes, and Tuek, and presumably several guards. Of course, he could have rationalised this, as I seem to remember him, in his internal monologue with Jessica, thinking about how he was rationalising what he was doing to the Atriedes, and recognising his rationalisation as such. He could have rationalised killing those people as being the Humane Choice, compared with what the Harkonnens would do. However, he never actually killed his client/patients.
I think that was longer than it needed to be.
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So he was actually saving people. Twisty rationalisations indeed, but theoretically true nonetheless. Very interesting indeed. 
Always so good to have another perspective on things.