I had a non-sme server compromised in a similar manner 2 or 3 years ago.
Since the pending outbound messages were (clearly) pure-d bona-fide SPAM, quite a bit of it was getting caught by "tarpit" servers.
A tarpit server will let your server establish an SMTP connection, then never let any traffic pass on that connection. Pretty soon, all of the configured out-bound SMTP connections are tied up by tarpits, and the spam host (your SME, in this case) cannot deliver spam (or email) to anyone.
One side effect of this was that the qmail service could not be stopped - because it won't stop while there are any open smtp connections, and the tarpits won't allow the connections to close.
In fact, I learned about tarpits by running netstat -an | grep :25.*EST, then doing some online research on the remote systems my server was connected to.
You need to find some way to disable qmail internet connectivity until you can get your queue cleaned out - either by unplugging your WAN cable or by some other means.
Finally, the advice about not playing with the qmail queue while qmail is running is mostly aimed at preserving valid emails that are in the queue while eliminating the unwanted emails. If you are willing to wipe out the whole queue you may have less to worry about...