And if this is technically difficult to do (because boards are not obviously linked to email addresses, or whatever), then that's still on them, but also solvable: allow you to remove BigCo email and just not give you access to any BigCo boards.
If you happened to have created a board yourself for BigCo, then that's still available to you. And if that's not acceptable for Atlassian, they should make boards more obviously connected to email addresses. Or something similar.
The equivalent to the current situation would be to allow you to add BigCo email to your personal Drobox account (for ease of logging in), and then remove you from the entire account when BigCo revokes your access. That's extremely unexpected!
The real devious behaviour was assigning your entire account to another entity to manage and without your permission. I've had to create a new account, ask the enterprise account manager to remove my account, and move my cards to another account. I've been using the account for 9 years and created many small integrations. Why would I want to give that up? Now my workflow is broken because the Trello app only allows one login so I have to decide is it going to be work or personal that I'm viewing because I can't do both.
If you're on Android, use Island or another app to set up a local Work account; you can now install a second instance of any app under the same profile, and log it into a different account. I'm unaware if iOS has similar.
Why? To me this is an obvious mistake. If you need to have sole control over your access to your account, then you should never attach an email to it that you don't control. You don't control your work email.
To me the sensible option is to have separate accounts for work and personal, and to never mix them. That way you're never even tempted to make the mistake of attaching an email you don't control--your work email--to an account that has your own stuff in it that you need to have sole control over.
This makes it seem like it's the third of the options I mentioned (personal account which happens to have a work email as an alternate email). But what you say a little further on (quoted below) makes it clear that it's the second: you used the same Trello account for both personal and work items. If the account had access to the company's boards, it's not just your personal account any more. It's a mixed work/personal account (which, as I and others in this thread have said, is not a good idea).
> As soon as I left the company and my email was disabled, all the boards under that email disappeared from my account.
But you apparently didn't remove that company's email from the Trello account. That's water under the bridge now, but in any case it seems like the company ought to be fine with telling Atlassian that you're no longer working for them and the email under their domain can be removed from the account.
What you seem to be wanting, though, is for Atlassian to just go ahead and erase that company's email from the account, or otherwise disconnect that account totally from the company so you can use it again, without any agreement from the company that that's ok. I don't see why Atlassian should do that.