I know this is an old post, but it shows up high in google when you search for a solution to this problem, so I shall give you the solution to this problem in the hope others will find this.
In Cairo Dock there doesn't seem to be a way to just remove a dock, but if you remove all launchers individually or move them to another dock, one by one, then once the last one is gone, the dock ceases to exist!
why the developers didn't just put an a command to remove the dock in one go, I do not know, but this method seems to work fine
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