I'm also running into this now, and it wont go away until I reboot my phone. I have all notifications disabled for the stock app, and have tried 2 other messaging apps to solve other SMS/MMS issues I'm having (wont send on wifi) and suddenly the stock app came back from the "dead" and won't go away or stay dead.
I can't even disable the stock app in the system settings like I was hoping I'd be able to.