You're absolutely right - this is an issue, especially for users who don't realise what's happening after running several big queries...
http://spbug.com/687 is tracking this issue at the moment; to address this we'll have to move some history to a file, or use gzip, or something similar.
(There's always File > Import for huge SQL; I can't imagine 500MB in the editor would be very pleasant either!)
Rowan
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