They used to be banned…back in June 2007 they were banned by the EU from flying into any European country. It was hoped that the ban would be lifted somewhere in October 2007, however by November, the EU refused to lift its ban stating that although reforms had been undertaken they did not satisfy the EU’s aviation safety standards. The ban was finally lifted in July 2009.

http://en.wikipedia.org/wiki/Garuda_Indonesia#2000.E2.80.932009:_Plummeting_reputation_and_EU_ban

Since then, the airline has been busy implementing its “Quantum Leap” plan…they have listed themselves on the Indonesian stock exchange to help improve their financial position, they’ve committed to overhauling their fleet and recently taken delivery of Boeing 777-300ER aircraft, which is due to be used on flights to/from London-Gatwick. In 2010, Garuda Indonesia signed an agreement to join the SkyTeam alliance, however it will officially enter in early 2014.

http://www.garudaindonesia.co.uk/london-flight-schedules-announced

I assume that the Liverpool decals that have been applied to the aircraft are simply for the charter flights to get the team to/from Indonesia and will be removed once they have returned…unlike the Man Utd and Man City logojets which are part of a wider and long-term sponsorship deal with the airlines that carry their names/logos.