Given how Alita behaves, I would imagine that she would want to destroy Godslayer, but at the same time I can't imagine her wrecking the planet doing so.
I'm guessing not killing the apprentice goes toward Benevolent?
Yep, you can consider it that way. There is also son of the merchant and that boar if you spare it. Also Ishkai trader and Sharok (betray or help).
Destroying Godslayer won't destroy the world, only lead to story of sequel. That means less magic, people are no longer born with macula or attuned to magic (shamans and mages). But if you do, you have fight few more bossess. That was no problem for me with Rogue class route, Way of Warrior, Berserk and Warlord X (lots of money). Also pay in mind that even devs stated it, the game is balanced ony in 1/3 or half and in normal difficulty.