The Empire and Canaan Moore are indeed allies, but not to the extent of intervening in each other's decisions. Even though the Elves now have only one Fifth Energy Level, it doesn't mean they are weak—in contrast, with the World Tree's main brain stabilizing the deity's seal, Averlyn, who can solely harness the power of the World Tree City, fears no one.
This is why they're bold enough to launch the Half-Moon Operation... As long as Canaan Moore's internal conflicts are resolved, the Elves' strength will increase instead of diminish!
However, in the end, Averlyn did not intervene.
The Second Generation of the Immovable Firmament is indeed worth her attention, but this strike... Hmph, if even with the control of the Fourth Energy Level True Dragon body it's unable to be countered, then there's no value in stopping it.