The previous posts are over kill security. In practice the federal police agencies fail to compromise
much less secure targets. I think that CIA/NSA would have trouble to compromise a target that takes the precautions mentioned, however they might stand a chance. However, I suggest people try their best to follow the tips even though they are currently not required to counter federal police.
Regarding Tor, the attacker does not need the cooperation of ISP or other external attackers. They merely need to do a sybil attack and add some nodes to the network. The attack is essentially the same as this one:
http://freehaven.net/anonbib/cache/hs-attack06.pdfThe tor devs added entry guards to counter this attack. However, there is a single entry guard between the hidden service and the attacker, the entry guards are selected from a pool of three nodes. So it is trivial for an attacker to find three nodes that have a direct link with the hidden service. If they can compromise one of those identified nodes, the hidden service is traced.