Really... How is integration with something like Jira a negative thing, how could it be? If HipChat locked out all non-Atlassian products, that would be bad, but they don't.
It makes arguing against the use of JIRA -- and all the project-management-oriented complexity it seems to bring if you don't keep a tight grip on it -- that little bit harder. Sure, not a negative for everyone, but has the potential to be the thin end of the wedge.