But isn't that how a lot of Star Trek stories have been told over the years? Something is introduced as a deadly, menacing force, but then turns out to be a harmless alien conducting a test (Balok), or a mother protecting its young (the Horta), or a soldier defending its territory against perceived invaders (the Gorn), or a grazing creature unaware that it was creating danger (the cloud creature in "One of Our Planets is Missing"), or a captain willing to risk everything to acheive communication (Dathon from "Darmok"), or whatever.
Or a potential ally that needs to be understood and respected on its own terms (the Vulcans, the Klingons, the Ferengi, the Cardassians, the Romulans, perhaps even the Dominion). Arguably, this is kinda the point
of Star Trek, and seeing it celebrated here just helped reaffirm the Federation's values post-Destiny
I really enjoyed seeing the conflict between Farkas/T'Mar/Fife's more militaristic view and the more traditional Starfleet ideals of Chakotay, Eden, and O'Donnell. After what the Federation has been through in the last decade, it makes sense that some people would shift more toward "neutralizing threats and establishing dominance" than "exploring and learning." The real threat wasn't the Children, it was Starfleet losing its way.