I love this idea. Even if it is pretty niche, that can be okay. Besides, it might not really be that niche anyway; we'll just have to see how it plays. And I think the need for spider form is just fine. If getting Ix early game is too rare and no one ever gets to enjoy the new god, you can make the altar untimed, guarantee a way to achieve spider form, or just remove the early game altar and force players to head for mid-game and spider if they want Ix. (Okay so the last solution is sort of like preventing the baby from crying by not giving it candy in the first place.)
You could leave spider hostile but re-flavor combat in that branch. Maybe Ix is trying to battle harden his champion and thinks a couple hundred spiders is a fair price to pay. In addition, since spider form doesn't eat and spiders don't drop anything except corpses, you could sometimes re-flavor killing a spider as "defeating" (full xp, full piety, no corpse, and the death message is different). You could be pulling your punches (fangs?) in melee combat. It wouldn't make a lot of sense to "defeat" a spider with an iood, so you wouldn't always be "defeating". Obviously, if you die, you die for real, but that's Ix, his spiders are individually disposable, and if you weren't tough enough to collect YOUR OWN RUNE then he didn't need you anyway. Arachne in particular (being intelligent and a magic user in her own right) could be sparring with you: maybe the fireballs you cook her with are illusions. None of this would change the gameplay. I think hostile spider in spider form would be cool, no other god lets you fight on your home turf.
Maybe bookend spider with some god messages; where he tells you to retrieve the rune as training, and to not worry about the collateral damage. He would congratulate you when you got the rune, at which point the nest spiders would become neutral. Or perhaps they don't become neutral until you escape from spider alive. (Metroid Crawl
)
Also +1 for a special vault with Ix in it down below Zot5. No loot, nothing to kill, purely decoration. Only for spider god followers. That would be sweet. Take the orb to him before the surface for a bonus message.
As for the creation myth: multiple real gods can each claim to have created life. Maybe one is lying, maybe they each really think they created life but are both wrong, maybe the real story is more complex (they worked together, perhaps unintentionally). Or maybe we just shouldn't worry about it, it's not a big deal.