Congratulations on your baby. This is a wonderful (and exhausting) time for you and your wife.
It's certainly not a time when you want to waste any emotional energy on negative thoughts. I think, if it were me, I would try not to read anything nefarious into her email. Just see if for what it is. A polite email by someone who doesn't think she's done anything that needs apologizing for.
I then would remind myself that actions are a better indicator of intent than words. Since she hasn't shown me any reason to think things have changed, I'd assume they haven't. Then I'd put it behind me, go back to avoiding the people that make me unhappy, and continue basking in the glow of my beautiful family.