Then, maybe the correct course of action for the EFF would be to work on improving the warrant system, rather than working on keeping alleged drug-dealing, unlicensed gun owners, illegal immigrants out of legal trouble?
That's what they are doing, this is how jurisprudence works.
Hadn't they challenged the warantless spying, it would have made a precedent in court. The police could have relied on the acceptance of the evidence in this case to do it again, anywhere in the US.
If the police was sure he deserved it and had the evidence to prove it, they should've just gotten the warrant. If they weren't, then they were just fishing and waiting for someone co commit a crime. And that's not just immoral, but against the Constitution.
What good does a warrant system do if the government doesn't follow the law? Trials like this are how courts get the executive arms of the government to follow the law. You'll notice that the presiding judge actively solicited a brief from the EFF.