Legally the four in charge of the Pirate Bay have done no wrong. They offered a file-sharing service which other people have used to commit piracy. It is these users who have commited a crime, not the four who should be punished. However, as it is not possible to arrest and prosecute all those who commit the actual crimes, the Pirate Bay crew are being punished and used to make a statement.

The problem with your first arguement is that suffering (pain, unhappyness, etc) and joy (physical pleasure, happiness, etc) are physical sensations caused chemically whereas good and evil are subjective abstract concepts. If a person were raised in such a way as they never experianced pain (amost certainly impossible, but for the sake of argument), they would still feel the same pleasure sensations from activies such as massage, stroking, sexual intercourse etc. "Good" and "evil" however differ between individuals. The majority of people would say the Columbine High School massacre was evil. However, there still exists school shootings; the V-Tech murderer referenced this act in the material he left behind, obviously this incident didn't result in him realising what is to be good (by popular standards at least).

I don't think you understood the second argument. Some studies have shown that there is neurological activity in the brain coordinating an activity before an invidual acknowledges that they are going to make said action. Differences between individuals can be explained genetically; an individuals genome expresses proteins in different levels and in many cases with slightly different structures than anyone elses. The different expression of chemicals in the brain determines personality, not choice.

Finally, the God presented by the Old Testement displays many qualities we associate as negative in people. His need to be worshipped, his acts of violence unto his creation when they displease him, etc.