she had every right in the world to call Peter out on this

Did she? Yes, he kept something from her, something important, but his reason for doing so was the usual, and fairly justifiable, one of superhero secret identities. He didn't do it to hurt her, or to spite her, but to try and keep her safer than she might well be if she knew. He certainly didn't do it to make his life easier.

I'd say it was comparable to certain real life examples like secret agents not being able to tell their family what they do for a living.