I promise you Atlassian understands why Trello is so successful. You described Trello's core strength perfectly - and this one of the reasons they are committed to keeping it as a standalone service.
(disclaimer: I'm the CEO of Trello)
In meeting with Michael, and discussing how we could work together, Michael could not be more clear that Trello's success is predicated on is breadth and its appeal to many different use-cases.
This is most clearly displayed in their inspiration page, that includes many, many use-cases:
https://trello.com/inspiration
Scott, CEO Atlassian
This goes right to the core of all of the issues/conflicts bundled into this acquisition from UX details up through to target users and culture clash.
Time tracking is a manager-oriented feature, not a producer-oriented feature. The users producing the work usually resent things like fine grained time tracking and comparitive producer reporting because it distracts from actual work, treats creative or complex processes as though they are part of an assembly line, encourages micro-management, pits quality against time, and emphasizes wage servitude.
Managers can use Trello to stress out their employees too, but not to the extent that JIRA-ish tools enable.
The problem is you are selling to managers who love to micromanage their employees and have nothing better to do than fiddle with configuration, reports, or have meetings with the people they hired to do that.
This is why developers who are smart will probably try to protect themselves by pre-emptively replacing Trello with one of the dozens of free or inexpensive clones before you can start corporatizing it and their company.
I obviously have no idea how Trello is structured and whether Michael has any real ownership or not, given its unique history, but in the case of most SaaS founders, when their golden handcuffs expire, they call in rich, because duh, why wouldn't they? Especially after watching the bureaucracy at the acquirer kill their baby.