Can't but help to feel that what you describe is a breakdown of both organization and work process.
It wasn't atlassian that "came along" - someone penned down an agreement and, from what it sounds, there was a lack of clarity both in regards to current and future principles of work and collaboration.
What we can do, as devs, to protect ourselves from the madness you describe is to be explicit about our work processes and their purpose.
Nothing much, but just a set of agreed upon principles and ways of working which should have nothing to do with tools.
What you end up with, by being explicit, is for having "something" to be supported by one or several tools.
Makes it easier to evaluate, select and change tooling that is fit for purpose.
