The gavel was struck three times in the courtroom on New Year's Eve, after the former intelligence deputy was pronounced a free man. The good name of Muchdi Purwopranjono, charged of masterminding the murder of a prominent activist, must be restored in full, a member of the panel of judges said amid the din and shouts of those who rejoiced, and those who despaired.

Now we're virtually back to zero – who killed Munir? He was found dead aboard a Garuda Airways flight en route from Jakarta to Amsterdam, where he was to study law. "I'd better study now, before I turn 40," he told this newspaper shortly before departing on that fatal day – Sept. 7, 2004.

Instead, at 39, he died of arsenic poisoning, found to have been administered by a friendly off-duty pilot who offered him orange juice. The pilot, Pollycarpus Budihari Priyanto was found guilty, but was later acquitted by the Supreme Court. He is now in jail for using a forged letter of recommendation from the State Intelligence Agency (BIN) that enabled him to join Munir's flight as part of the airline's security staff.

Finally, investigations resumed and Muchdi was brought to trial, implicated through his alleged frequent contacts with the pilot and his role in formulating the letter of recommendation for the CEO of the national carrier.

But on Wednesday the judges of the South Jakarta district court said none of the evidence presented in court was strong enough; the former pilot responded by saying that he would immediately enjoy his freedom again. "All the reasons cited for jailing me are the same reasons for charging Muchdi," Pollycarpus was quoted as saying shortly after the end of Muchdi's trial.

Wednesday's verdict must be respected, as Munir's close associate Usman Hamid said, "but it is difficult to accept." Following the verdict, his widow Suciwati said that, "I have lost Munir and now I have lost justice."

We support Munir's family and friends in further pursuing justice, by attempting to hold to account whoever is responsible for Munir's assassination. When the Supreme Court has its, the final, say, it is anyone's guess how it will decide, given that the lower court basically treated all presented proof as circumstantial evidence.

It will be up to legal experts to debate whether indeed the state prosecutors did their job, or whether more willpower and insight on their part would have probed beyond what they alleged was merely Muchdi's personal motivation of revenge against Munir.

Munir's case, as suggested earlier by President Susilo Bambang Yudhoyono, was, and is, a test case "on how much Indonesia has changed."

Munir and his colleagues intensively pursued cases of "state violence" – violence involving the state apparatus and/or state institutions – including the kidnapping of activists towards the end of Soeharto's rule, for which members of the special elite forces of the army, then led by Muchdi, were found guilty. Therefore prosecutors looking into Munir's murder looked for motives within the circle of security forces and their sympathizers.

But the pilot and the former intelligence deputy said in their defense that the charges were ridiculous. Moreover, a crucial witness, Muchdi's superior, then intelligence chief Hendropriyono, did not appear in court.

At the dawn of 2009, we therefore have no answer yet on "how much Indonesia has changed" for victims of violence, particularly at the hands of the state, nor concerning a citizen's safety and freedom from fear. In court, Muchdi's supporters wore T-shirts warning us of "foreign intervention". But we fear more for the safety of civilians here, with or without foreign interference.

As the case has not been put to rest, the ordinary civilian would still have to ask themself: Is it safe for a civilian critical of the powers that be to board state-run public transport? How secure are people working on sensitive cases involving security forces?