Once you put an NTP server on the 'net, it's public - pretty much like most Web sites. Sure, there are reasonable expectations of decency like for anything in the Commons, but I don't think there's any legal defense against skunks at the picnic.
IIRC, the university called Netgear out for doing something stupid and disruptive, and Netgear stopped doing it. The second best possible scenario, I guess.
Netgear issued patches for the devices. Most people never update their server firmware, and we're talking about over 700,000 devices. The university still gets considerable traffic.
Throttling won't do much good; their WAN interfaces will still eat the traffic, I don't think it's as much of an issue that the NTP servers were melting it's more that their entire network was.
For what you want to have any effect they'll have to sinkhole/throttle the traffic upstream before it ever reaches them and as a university they are effectively an ISP so that might not even be really possible.
It'd be interested in seeing if there's been any update since 2003.
E.g., is it really "considerable traffic" by 2016 standards? The original flood in 2003 was 150 MBps - I don't think I'd notice if I got a flood of 150 MBps on my home connection.
How many of those devices are still around 13 years later?
Wow, I never realized operators couldn't push fixes to their routers without permission. The internet is indeed a tragedy of the commons: trivial to ruin, but a Sisyphean task to fix.
Most admins would consider having network infrastructure's firmware change outside of their control a bug/misfeature. Not to mention most devices would require reboot to apply change.
And to be able to remotely change the code running a HUGE security issue.
The vast majority of admins don't even know that they're admins. They bought or received a cheap Netgear router, plugged it in, and never touched it again, except to maybe turn it off and on again when the internet was slow/down.
If you're an admin who cares about their infrastructure, you're not using a bargain-basement Netgear router, and if you are, you'll have gone through every single menu and seen the auto-update option.
Some operators do, mostly ISPs that lease routers to customers and retain a way to push firmware updates to them (for example, Comcast does this). But router manufacturers typically don't touch the device once it's out of their hands.
Note that cable modems (all of them, not just from Comcast) download their configuration from the provider every time they boot up. Ironically (since it uses TFTP, for one), this is called "secure provisioning".
They might give you a web interface where you can configure certain settings (e.g. integrated Wi-Fi) but the ISP ultimately has at least some control over any cable modem connected to it.