Starsan will sanitize the outer skin of the cherry as long as the cherries were clean to begin with.
Thanks. Last question on the subject: I’m thinking of doing a Belgian blonde style base with the cherries in secondary. What is everyone’s thought on a brett spp. like bruxellnesis in secondary w/ the cherries?
Brett in secondary = yummy.
I can’t comment on the cherries because I have never used them, but I can comment on the contamination.
Work on getting over you parinoia, my brewing brother. It is holding you back. In 26 years I have never had a contamminated batch and have done every unorthodoxed thing you can think of to beer; going elbow deep to retrieve O-rings & thermomters, forgetting to put the lid on the bucket for several days, etc…
I’ve dumped a few that were un-drinkable, but not due to contamination ;D. My next, or current one, may become so because I am due. 
But I have been able to make some good and interesting beers because of it.
A sensable approach to cleanleness and sanitation and understanding the difference is all that is required.
I have never heard of a batch being contaminated due to dry hopping. Not saying it hasn’t happened, but contamination was probably caused by something else and was going to happen anyway. No cause and effect to quantify here.
On the next batch you want to dry hop, wash your hands, take out the hops, close your eyes and take a deep breath and set both the hops and your brewing spirit free. 
Another thing about cherry pits via kirsch entry in the Encyclopedia Britannica:
[quote]kirsch, also called Kirschwasser, dry, colourless brandy distilled from the fermented juice of the black morello cherry. Kirsch is made in the Black Forest of Germany, across the Rhine River in Alsace (France), and in the German-speaking cantons of Switzerland. Its production methods remain traditional. The fully ripened cherries are mashed in a large wooden tub or vat and allowed to ferment freely. Upon completion of this process, the entire mass—liquid, pulp, and cherry stones—is distilled in a pot still. During the mashing some of the cherry stones, or pits, are crushed, releasing some of their oils and acids. These include small amounts of hydrocyanic acid, which impart a distinctive bitter almond undertone to the beverage. Kirsch is not aged. It is marketed at 90 to 100 proof, in the clear white (colourless) state it comes off the still. It is a fruit brandy with a clean cherry fragrance and bitter almond taste. Kirsch is consumed neat, as brandy, and in cocktails and is also used in cooking as a flavouring
[/quote]
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So maybe less worries about cyanide when pits aren’t crushed?
- Mike
No interest in poisoning myself with something (or at high levels) that my body can’t handle, but if our bodies can metabolize small amounts of these toxins, then it begs the question: Can yeast (saccharomyces and brettanomyces sp.) and bacteria (pediococcus) metabolize these toxins? It would seem that they can.
http://www.atsdr.cdc.gov/toxfaqs/tf.asp?id=71&tid=19
http://www.atsdr.cdc.gov/ToxProfiles/TP.asp?id=72&tid=19
One thing to think about with trying to get more flavor out of your cherries… freeze them, once thawed, give them a light crush, just enough to kinda half way juice them, take that juice and boil it down to a syrup then add that to secondary with the cherries… should give you a stronger flavor.