I am using the 555 in a missing pulse detector circuit. So I only need to know when the output goes low. I don't need the high output signal from the 555.
So, why not use pin 7 of the 555?
This has the same logic polarity as pin 3, is open collector and there are no diodes or bias to the 555's Vcc.
The MCU pullup would be fine, or throw on your own to 3.3V
(Of course we can ask why you're using a 555 at 12V.
You could use a CMOS 555 at 3.3V.
Or even just a CMOS Schmitt trigger.
Or do your missing pulse detection in software.)