There has been diving allowed on Santorini for several years and Alex Sotiriou has Volcano Divers, one of the two. It looks like the diving was so good on Santorini, that one of the two operators sold his operation. These are mainly tourist operations using zodiacs to get them in and out of nearby sites quickly, and although I know Sotiriou's people are excellent, the dive sites aren't up to the standards desired by most experienced international divers.
http://www.scubagreece.com/index.php4 (Alex Sotiriou)
http://www.diveclub.gr/ (looks like Chris Pozides sold it recently)
Yes, I am one of those who suggested that people who associate all the other great things in Greece (ruins, beautiful islands, friendly people, etc) to diving in Greece might be disappointed, and I don't like to build up people's expectations. Better to downplay and then they are happier. Because the lack of fauna and flora which has gone down due to the illegal spearfishing, not to mention the dynamite fishing in remote areas (you MUST have a lookout!)
Also I told people to be careful because the rules were changing at the time I was there. I based my opinion on talking to the Ministry and also diving several times with local divers who knew the best places, in Attica, Milos and Crete during the Winter and Spring of 2001-2002. But I have not dived all of Greece, after all, we have many hundreds of kilometers of coastline. I'd LIKE to, but first checking all the laws and logistics required.
I would not be surprised that they have opened up the diving now (money talks and tourism has been down), and certainly if you can FIND a licensed operator nearby, you are in luck. Otherwise you must go with a private group or club. I would thoroughly check out the laws before jumping in a boat to go to a site with someone lacking liability, etc.
I love my country and think Greece's special offering to international diving might be the WWII wrecks that are strewn around the islands, which have historical value. For example, there are at least half a dozen such wrecks in the harbour of Milos not to mention Souda Bay in Crete. Unfortunately, the Port Authority will pick you up if you try to go out to them. And it is very dangerous to go in a zodiac with no backup or hyperbaric chamber, etc, etc.
As was said, the port authorities have been told that divers want to steal antiquities, but those attitudes are changing as the old guard retires. When I was in Greece, all you had to do was preregister your dive trip and C-cards.
But, the new diving areas have to support a profit. The fellow at the Ministry of Merchant Marine Office, stated in an article, that maybe one hundred dive operators would be opened in Greece, now that the rules were changing. Surely, only a non-businessperson, non-diver could make such a comment.
If Manos can find me a dive site which is easily accessible to tourists, and close to Athens for safety and convenience (like Hydra but that island has been taken) has diveable wrecks OF IMPORTANCE (not those little scrap heaps) that are now LEGAL to dive, I will return to Greece and set up my dive center. Please note, don't go this summer because the Olympic Games make getting reservations in Greece and getting around there, very difficult.
On a brighter note, if you go to Greece, you might keep going and check out Cyprus. They have what looks to be a very active dive scene, and it is home to a very diveable wreck, The Zenobia, which is probably worth the trip.