First, according to TFA:
Neither May First/People Link or Riseup was not notified that the server was being replaced. It was never notified that the server was taken in the first place.
In order for a warrant to be "properly adjudicated," it is required that the law enforcement agency serve the warrant to the property owner. By not notifying the property owner of the warrant, they violated the 4th Amendment.
Well, if they were renting space on a server owned by the hosting provider, informing the hosting provider is probably sufficient as they are the property owner for the server that was taken. I don't know if that's the case, but it is possible that this particular item is not a 4th amendment violation.
The FBI has a long history of blatant violation of civil rights, as well as literally making criminals for the sake of "busting" them, thus justifying their existence (which, in government doublespeak, translates to "budget"). That said, it would be more surprising to me to find out that the legal rights of the property owner were honored.
I would say, even without a pretty well documented history of the FBI abusing its power, it is generally a good thing for people and organizations to watch and question the actions of any law enforcement organization; especially if something looks amiss. It keeps them from getting lazy and it keeps us from getting caught napping by those whom we give power.
Trespassing is illegal; any evidence gained illegally cannot be admitted in court; therefore, if the FBI did indeed trespass, then any case they may have had is now dead by their own hand.
Actually, I don't think this is entirely true. In 2009, in Herring v. United States, the U.S. Supreme Court held that illegally obtained evidence could be used in court as long as it wasn't deliberate, reckless, or grossly negligent conduct that led to the evidence being illegal. (that case was about a man who was arrested on a warrant that was left active by a clerical error. When arrested he was found to have drugs on him. The court ruled the drug evidence could still be used against him even though they had no proper cause to search him and find it in the first place.)
I expect you will argue that in this case it meets the deliberate, reckless, or grossly negligent conduct requirement; and that may be true. I am not saying their actions wouldn't invalidate any evidence they collected. I'm just saying that there is an avenue for them to argue to keep the evidence, even if it was determined they had violated the 4th amendment in collecting it.