You can actually just get away with unchecking "mail" from the sync list. Bit less intrusive.
I also found the path you gave to vary slightly - ~/Library/Mail/V3/random-guid-id/[Gmail].mbox/Spam.mbox - still eminently discoverable, however. This was on El Capitain, and I realise this was on the ML forum...
Another fun gotcha - my Mac was able to sync IMAP despite IMAP being disabled on my gmail account. I had to enable IMAP in order to see the "hide" checkboxes, and uncheck "Spam". I am now contemplating disabling it again, just for fun.
Now for a life with 99% less grinching from Sophos 😀