...Because I am freezing them, I am sure that most of the wild yeast and micro-organisms will be killed off...
Freezing won't 'kill' most microbes. It may lower the viability, but you'll eventually get wild yeast/bacteria growth when you bring it back up to temp.
If you want to utilize the wild yeast, wash with cold water and use them whole/fresh. If you have to store them, get a culture going before freezing: drop a few fresh cherries into a quart of starter wort.
If the starter isn't to your liking, or if you decide against a mixed ferment, puree and sulfite after thawing.
Don't worry about pitting. I would take the stems off, though.