Yeah, their stickfigure-like bodies have been proven as a canon anatomy, so as such, that just makes the spider attempting to bite her even harder ‘less it’s the head.
And as for the fight, it might be true that one bite from the spider means Ellie is done for, but as I mentioned earlier, it will have a hard time trying to sink its giant fangs against Ellie’s stick-like body. And given the spider‘s appearance as well as the fact that it is still an animal, Ellie would be smart enough to know not to get in front of it. She does have wings which she could use to fly up and potentially over it and attack it from behind to taze it with a taser or stab it with a knife.
On top of this, she has the LS advantage which is useful for holding it back from biting her.