I guess that's one way to lose your customer base. We have a team of 50 that will be switching to another platform shortly. Good bye HipChat...
Atlassian themselves could snoop on your traffic; the only thing stopping them is their terms of service. All you have to do to protect your employees is publish clear guidelines on when and how your company will access employee communications on company-owned infrastructure -- bingo, problem solved.
It's nothing but a policy that prevents your SaaS provider from reading your data in the first place.