The first film makes mention of Mormon "extremists," whereas in this film, the whole Federation gets religion. It's not so much that God's back, He never left.
Until the Marauders appear, human weapons are much less effective than in the past, and of different models. The Federation's Sky Marshall has been brainwashed into turning traitor. If it's a coincidence, it's a funny one.
During the crossing of OM-1, Behemecoatyl kills doctor Wiggs first. Wiggs could have declared Anoke unfit for duty, and Lola was pushing him to do just that, so he took him out because Anoke was still useful. He could have also killed Lola... Except she's the only one present who knows the location of Sanctuary, an information that could destroy the Fleet if leaked, and he likely knew from Anoke through the captive Brain.
The Federation's most sacred tenet is that service cannot be compelled. It has to be freely given for the good of society. For them to violate that by instituting conscription means they've crossed the Godzilla Threshold.
