The CEPT TR61-01 document under which you will be operating does not have a separate prefix code for Crete. Only the standard SV/ for Greece. However as the locals are all SV9 - your use of SV9/ seems logical although not specifically stated in 61-01.
This would also be in-line with operating in Australia under the CEPT arrangement where one operates as VK2/ in NSW, VK3/ in Victoria and so on although in the CEPT Document the prefix for anywhere in Australia is given as just VK/.
Basically the local laws override the CEPT agreement in this area.
So I believe you will be correct operating as SV9/OM4WY/P.