Killing small, parasitic critterst shouldn't be a problem, since they're non-sentient, potentially lethal and most of the time, hostile. About NPC's, the subject changes entirely, and I'm against killing random NPC with no reason. Of course, there should be the option of taking care of a particulary danguerous foe, but only in a context that leaves the PC with almost no choice, or to make the plot a bit more serious and/or dark in some points.
Still, it should be given only as an option, not as the default choice, for those to pursue lighter paths. On my mind, those NPC who deserve or may be subject to this (optional) treatment may be Jack (not sure about him, since he's more a spoiled kid than anything) Uncle Max (two cesars are one too many!!), Amara Faell (it was boud to happen, given her lifestyle, and she deserves it because stunlock), Miriam Bragga (again, dangerous lifestyle, and even worse criminal behaviour than the former).
Those who can be killed at the moment are HandSo (I don't think that it counts, since it's machine, and a quite dangerous one), Taivra (a punishment a bit disproportionate), Shade (it may sound harsh, bout her death may be for the best if we want have the whole of the inheritance, and hey, we're not the ones who killed her, after all), Zaalt (again, unfair, and unlike Taiva, he wasn't attempting to harm us on his own), ah, and the Myrellion people, this one being simple and act of stupidity from the player against a large number of NPC's. The same can be said about Tarkus, except that we didn't bring the bomb in the first place, and the losses, tought equally unfair, were fewer (the dissapearing of the gray goo isn't exactly a loss, since they're considered a plague).