I'd replace the homepage (temporarily) to the absolute minimum during the time it's bombarded with requests, unless you have a vserver/cloud-host that you can scale up. Or change the server your DNS records point to, if you use CNAME, to one at rackspace, github homepage, or anywhere else with a minimal homepage. But I'm sure the guys @HN have better tips :)
I don't know much about legal stuff and licenses, but I would allow anyone to use your software as long as it's code is shared, except for enterprises. Companies who want to use it commercially and have more than 1-5 employees would need to obtain a license. Open Source doesn't mean that you cannot put a price tag on it.
But as you said, prepackaging the stuff as a deb/rpm and allowing white-labeling for enterprise customers would be a good way get some money back from this. Just saying, but you could, if you wanted to, add advertising into the opensource product and disallow it's removal unless a license is obtained. If you were an SaaS, you could collect data and metrics, that you could monetize, but I'm glad you aren't anymore :)
@pg I think there should be a sticky informing website owners on howto react, when their website is HN'ed. Somewhere in the footer of the homepage or so.. This is happening a bit too often and many aren't prepared for such high traffic peaks.