There isn't much you can do to prevent fungal infection (if you don't want to spray) other than using clean, sharp tools and pruning during a time when spore loads are low. You'll probably be fine - just don't make a habit of pruning your stone fruit in winter. PNW winters are warm and wet, which promotes fungal infection.
Here is a nice summary of pruning rules for sweet and tart cherries:
http://www.which.co.uk/documents/pdf/cherry-pruning-153955.pdf
Basically you need to answer these questions:
- at which age do branches bear fruit?
- do they fruit on spur systems, the length of the branch, or tip of the branch?
Then you prune to maintain and rejuvenate accordingly.