Where's the downside to this? The unrelated sites suffer maybe a few hours downtime max, and they don't have to worry about tipping anyone off.
If the FBI is already there, it really shouldn't be a problem for them to locate the exact server that hosts their alleged offender and confiscate only that one.
How do you think anyone would be tipped off in that situation?
For example, I believe it's illegal to take information which was coincidentally seized along with legitimate evidence subject to a warrant, and use it in an unrelated case. I'm strongly in favor of such laws, to discourage "fishing expeditions", where law enforcement uses a legitimate warrant to seize a bunch of unrelated material that they're interested in using for other purposes.
However, I suspect if you walk into a data center where some malicious customer is doing something illegal, probably that customer has tried to make it harder to connect them to what they're doing.
Also, I don't know about this case, but there are lots of small hosting companies that lease servers from other companies, and the staff at the colo only know the lessor, not the lessee. They wouldn't have any access to the hosting company's customer database which might map customers to servers.
Besides, the FBI has to worry about low-probability cases like, what if one of the employees is a friend of, or paid off by, the bad guys? Or what if the bad guys are somehow monitoring the facility?
The FBI has a legitimate goal of seizing the evidence they need as quickly and with as little notice to the bad guys as legally possible.
Did the FBI act wrongly in this case? I don't know enough to tell.
That is exactly what they are worried about happening.