Umm... where to begin.

I can understand where you're coming from to a point, but what you're asking for is quite silly. With the logic you are bringing in one could say that Killing Virtual animals in the game is blashphemous to Vegans, or fighting other people is blasphemous to people who have taken a vow of peace and there should be no killing in the game. It may as well be a Farming Simulator at that point, with only plants as farmable goods.

This is a Game, any use of Real Life names are strictly a nod or homage and not to be taken literal. Hell Shiva and Garuda are female in the Final Fantasy Universe. Next I assume you'll be wanting to take out all of the Voidsent especially those with Biblical names because Christians will feel like they are ungodly and shouldn't be represented in their media.

Also Remember, for the most part, the Beastmen have summoned their Primals as a reflex to being attacked by the Garleans. Their Primals are not Benevolent but act the way they do due to the feelings of their followers at the time of the summoning. So if they are painted in a different light than you'd expect, it's because they have been called for under duress and are acting as such.