But I do feel that at some point I should make it clear where I stand, and she seems to have opened the door for that.

An open door would look more like this...

W: "Gerk, do you really think we can fix our M?" or "Do you really think you can truly forgive me?"

It does not look like this...

It is "irrevocably" over.

If you decide to state your intention be prepared to get slammed.

FWIW: I like Jim's version better..."I understand how you feel, but it isn't over for me."

That way, you've acknowledged her feelings, and simply state where you are at. I'd probably place it as a PS in your email. So it is set apart from the lighthearted chatter in your email.