I don't get why this is such a thing of contention. Its not like Ellie is breaking into homes murdering people's pugs and beagles. She's fighting off dogs that are trying to maim/kill her, or lead humans that want to do the same to her location.
Earlier today I played Fallout 4 and killed around a dozen dogs with a shotgun. Shredded a bunch more with a minigun, punched another while I was wearing power armor and its head literally exploded.
Where was the outrage for that game? Or Fallout 76 where you can do exactly the same kind of stuff?
And before anyone says 'but those are mutant/rabid dogs!' not all of them are. Fallout 4/76 are full of normal rottweiler-style dogs attached to the raider factions.