But he IS evil, especially from the point of view of the Atreides. The capitalized word makes it so! Plus, I could repeat it and make it even more of a truth!
I only read the lines as meaning he wishes he could avoid causing such pain to royalty, as we later learn that he doesn't wish for Leto to be seen by others in such a state as when he is drugged. Sets bad precedent or some such. Nevermind he is a distant cousin, it's all about royalty being seen in a bad light, not wanting to give any ideas to others in his household I think. (Like that one line in "Unforgiven", where English Bob says someone trying to assassinate the Queen would tremble at such a thing and be unable to do it. Sort of the same principle, but remove that initial hesitation, show that such a thing can be done, then killing royalty isn't seen with as much difficulty. I would refer to the assassination attempt by Feyd later on as case in point).
Baron says that he must have the Atreides line ended. His thinking is twisted, when he says that the other Houses must know it was his doing, thus he must have Leto: they would know anyways, considering the long-time feud between their Houses. Baron says himself, they will know. Instead, he wants to gloat over Leto, even brings him to the dinner table for display later on. He wants to rub his face in it, so to speak. How cruel is that, a drugged captive sitting at the table while they have dinner? And you know it was a fine setting, crystalwear, servants on-hand, multiple courses being served, and a drugged captive sitting across from you. Sounds wicked to me....
A knife in the back of Leto would have been a kindness, but that's not something the Baron is known for, kindness. The things we learn, his treatment of the Fremen, his torture of Duncan's family, the enslavement of Gurney, these things of which we don't know the particulars, all show the Baron to be a wicked, evil man. The way all these different people react to anything Harkonnen, shows the great hatred he has brought about. It seems that he had a talent for it, or a natural disposition.
That there was a sad tone in his voice to me shows how overwhelmed by his own wickedness he is. That he may feel a bit of sadness but still follows through with his plan, shows that his thinking/mentality is flawed. To feel one way, but think and act another regardless of one's own feelings, to me shows dishonesty with one's self, even internal conflict perhaps. Maybe it's just that his gut feelings are too far buried under the fat!