Microsoft presented the need to take control of this cluster of malicious domains as a necessary action against the Nitol botnet and to protect and secure the supply chain. While I don't quite understand all of the logic behind this argument (there's just not enough info public at this point in time), at the end of the day Microsoft have managed to remove a thorn from the community's side.
The Nitol botnet is, in general terms, bothersome but not a wide scale threat. Damballa Labs has been tracking the threat for quite some time and, as botnets go, is a rather small and tired affair. If you're a victim of Nitol though, yes, it's a pain-in-the-bum DDOS agent.
The 3322.org angle is much more interesting to me than the Nitol botnet that formed the legal excuse for being able to seize control of the domain.
From a Damballa Labs perspective, we currently track around 70 different botnets that currently leverage 3322.org's DNS infrastructure for C&C resiliency - using a little over 400 different third-level domain names of 3322.org. With a bit of luck I'll have some size information about those botnets later today.
Will the usurping of 3322.org kill these botnets? Unfortunately not. There may be a little disruption, but it's more of an inconvenience for the criminals behind each of them. Most of these botnets make use of multiple C&C domain names distributed over multiple DNS providers. Botnet operators are only too aware of domain takedown orders from law enforcement, so they add a few layers of resilience to their C&C infrastructure to protect against that kind of disruption.
Take Nitol for example - it employs multiple domains from several free dynamic DNS providers, including other four-digit .ORG domain services such as 6600.org, 7766.org, 2288.org and 8866.org.
Interestingly enough, the (former) owners of 3322.org are providing new support advice to their inconvenienced customers in how to bypass this interuption by Microsoft:
Or, after some Google translation:
Good to know that it's business as usual...