Okay, seriously, what the heck Wonder Woman? There's some fundamental disconnect here.
I think that's the problem everyone had with canon, and it's shown in full, glaring view here. Just what were they thinking? From the surface it appeared as if their thoughts went as far as 'Whelp, Zatarra's gone, that's our major magic user down, thank goodness Doctor Fate is here to pick up the slack; let's get him inducted quick so we can work on our cover story for Zatarra,' and no further. You think 'that can't be it', but you dig deeper and... yeah, that's pretty much it. They were aware of what Nabu did, how repugnant it was, and how it affected the people around him, but it seems as if they just wrote him off as dead immediately and compartmentalized the rest away. They justified it to themselves and welcomed Nabu as a friend an ally based solely on his record, which, admittedly, is suitably heroic aside from a few dark spots.
Now Paul killed him and a man they thought dead is back and they don't really know how to handle it. Diana tried talking to Paul, but it seemed to me more as if she were trying to adjust Paul within her own personal world-view, trying to make him 'fit' as it were. She all but asks him to prove to her that he isn't a villain, and he turns that around on her and asks her to prove
she isn't one, all while pointing out that everything he did was perfectly legal, while what they did was most certainly
not. Then he leaves her without her being able to justify it to him, and indeed, herself as well. Paul robbed Diana of her chance to reaffirm her faith in her decisions, and instead left her to ponder the rightness of her actions.
It's been said before, but I think it needs to be said again; this is a flaw of perspective as much as anything else. In the League's eyes what Zatarra did was sacrifice himself to save his daughter, something perfectly in line with their world-view. What Nabu did was rationed away as a Hard Man Making Hard Decisions, the needs of the many outweigh the needs of the one, there must always be a Doctor Fate, etc. It was easy to accept when they didn't have a body, easy to accept when Zatarra was still
technically alive in there, just doing more good than he ever could on his own. At great personal cost, yes, but again, this isn't something strange for heroes. There was no one argument that convinced them what Nabu did was in any way okay, instead, they chose to view the circumstances in the best light possible and slowly rationalized their guilty conscience away until it no longer bothered them, until they had accepted that this was the new reality. And those who didn't see things that way were convinced at seeing so many of their friends and colleagues, people they respect and look up to just... go along with it; because surely they know what they're doing, right? And then Paul comes in and wrecks pretty much everything, now comes the time when they take a long, hard look at themselves.