Well, assuming any of them are real real and assuming Pate is dead and no longer a danger to anyone.
Honor, justice, morality, being practical, and various higher, advanced thought-pattern sentiments. Clothing and feeding a freezing starving immature being of one's species is likely fairly clearly on the side of some more absolute good, something just and desirable, as it would be the other way around should the recipient of such benefit murder their benefactor for some willful but arbitrary reason. That's all somewhat more subjective at some times than others, certainly, requires awareness and intent and understanding. Also, something like willfully torturing Ardent for hours for your own amusement is on the evil side of things, as would be betraying your closest ally on a whim or for an amount of money you'd consider trivial, even if it had been foretold, even had it been desired. Not that some don't have a moral compass that works off of something more like anti-magnetism, not that some wouldn't agree with or side with such.
So then, what is the difference between an unwilling dupe harboring no ill-will and a knowing manipulator attempting to reach goals by any means needed regardless of who has to be hurt? A cooperating potential danger in a somewhat known way versus a confrontational variable danger of unknown quality, there appears little correlate. Not a fair thing to treat them equally, we might say. Laws here and now, what system is that within? Seems in this situation, Alice and her task of doing what she thinks best for everyone as a whole. Altruistic, hopefully moderated by some higher goal rather than personal desire. Her behavior seems so, at least out here.
Still, laws in general don't always stop all behaviors they ostensibly mean to, they instead (when they fail to guide and push into conformity) mostly codify the consequences of behaving in ways that are undesired. Laws in a social context, behaviors that are damaging to society. Although some societies have different ideas of what evil might be, and similarly, some other society may just come take them to task for how they operate. Potentially put in something worse. One has to have intent though. Free will, choices, understanding of actions, seems required here in such abstract things. Regardless of how interesting the idea of evil horses or chickens is.
In any case, executing Pate for unleashing Church upon baseline humans. Seems potentially fair. But wait there's more. For kidnapping four others including yourself. Even more so, for just recently basically ordering Church to go kill you. Perhaps what Alice probably just did isn't "good", yet maybe somewhat justified, and probably a sort of justice for at least one murder Pate could have been counted as responsible for. Again too, if Sedna is permanently out from having to get rid of Church because of Pate. Demonstrably, there are a lot of reasons to consider Pate a greater danger who simply isn't currently in a position to do anything more. Call it preemptive. Or simply a delay, a bit of explanation before the already moving executioner's axe hit its mark.
If Alice is whatever destroyed everything in the Blink, as she just said, it appears more and more like some expected result of bleeding off something like what might have been "the event horizon having no surface left to store anything" and Alice being the one who released it to even everything out. Reversing the irreversible, reducing the number of chances that normally only increase, shoving the genie back in the bottle with a rusty spatula. Not what she'd have wanted perhaps, but better than the alternative probably. Which if these habitats like what they're on were the arks of sorts put into place by her before carrying out that unfortunate but necessary action of flooding the world, that doesn't necessarily make her a villain, and it could even make her a hero. Not that she doesn't feel bad about being the one who crushed the car so its metal could make a new one.
Nothing is wrong with Pate wanting more for humanity, perhaps he is correct. Maybe his idea was workable, and would have left the Earth some paradise. Or maybe he and Church would have taken over what's on Earth and in space and made everything far worse, heaven run by cruel manipulative sadistic overlords. At least until Pate died, and then only Church. Either way, Pate's methods seem to have left much to be desired, and even if they were good and pure in intent, he appears to have paid for the manner of their implementation.