Earlier quoted context omitted.
Author here. I don't think it's malice on their part, but their hammer is too big to be wielded so carelessly.
IMHO, it sounds like it worked. The things you changed sound like it's made your site more secure. In the future, Googles hammer can be a bit more precise since you've segregated data. And you don't know what triggered it. It's possible that one of your clients was compromised or one of their customers was trying to use the system to distribute malware.
No significant security is introduced by splitting our company's properties into a myriad of separate domains.
This type of incident can be a deadly blow to a B2B SaaS company since you are essentially taking out an uptime sensitive service that a lot of times has downtime penalties written down in a contract. Whether this is downtime will depend on how exactly the availability definition is written.