Earlier
 

Anonymous had earlier issued a statement "warning" the Turkish government that it should stop its acts of Internet censorship which, according to the group, were "in violation of basic right and freedoms."

Should it be like one of two below?

Anonymous has earlier issued a statement "warning" the Turkish government that it should stop its acts of Internet censorship which, according to the group, are "in violation of basic right and freedoms."

Anonymous had earlier issued a statement "warning" the Turkish government that it should have stopped its acts of Internet censorship which, according to the group, were "in violation of basic right and freedoms."

Re: Earlier
 

No - the original is fine.

a) "Earlier" presumes you already have a reference point in the past. Here the full text of the original is : ...three of its members were arrested Friday in Spain. Anonymous had earlier issued a statement ...So, the reference point is Friday when the 3 members were arrested. The use of the past perfect sequences the action as having occurred before the reference point. Compare : When we got to the airport the plane had already left. The reference point is the moment we got to the airport. The use of the past perfect tells us that the plane left before (earlier than) that point.

b) The second verb could be either are or were, but were is more likely here :
- are is possible because the views are still true. This might be used in spoken English
- were is possible because this is a report of what Anonymous said 24 hrs ago - ie it's an opinion expressed in the past. Written English tends to keep the use of tenses uniform - if the event happened in the past, then what is said is also reported in the past - so in this journalistic article it's not surprising that the past was chosen rather than the present.

c) No. If you say should have stopped then the time of the "stopping" is past (the perfect infinitive indicates a past event). For example : I should have completed my tax forms yesterday - but I was too tired.
But Anonymous are saying that they want the Turkish government to stop censorship now/in the near future - therefore the simple infinitive, which expresses present/future events, is correct.