There are some good counter measures. CloudFlare, the CDN that I'm using for my site http://gitignore.io helps mitigate DDoS's [1]. Github also took a good step by separating the source code domain github.com from the pages domain github.io [2]. I agree that tomorrow Atlassian could suffer a DDoS attack but I feel like since they are a more mature company, they have a lot more experience dealing with that type of attack.