no matter how I unsubscribe from the folder

Can you describe in detail what you did?

- Right-click on the account, click "Subscribe" - Scroll through Folder List to Gmail/All Mail, uncheck box - Click "OK"

Also:

- Right-click on the account, click "Subscribe" - Scroll through Folder List to Gmail/All Mail, select folder, click "Unsubscribe" - Click "OK"

I'd check for "synchronise" too. If the All Mail folder is chosen for synchronization, this may override the subscription setting.

Subscribe lets you see a folder. Synchronization makes a local copy, which is what I think you want to avoid.

I've unchecked "Select this folder for offline use", but that setting does not survive after I unsubscribe from the folder. It is reset to a checked state once Thunderbird automatically re-subscribes to the folder as described above.

I don't know why the setting wouldn't stick. This may be a long shot, are you using CCleaner or something similar and do you let it mess with the Thunderbird profile?

I'm not. I suspect the setting doesn't stick because once I unsubscribe to the folder it deletes the local store entirely. I presume the synchronize preference is stored there rather than in a global setting.

For now, I'm subscribing to the folder and disabling synchronization; that's less than perfect because it still downloads 100k headers, but it's better than attempting to resync the entire folder.