Welcome to the Wefugees community and thank you for your question.
Your girlfriend is an EU-citizen. Therefore she can travel to Greece easily and get married with you. That shouldn't be a problem. Since I'm not familiar with the marriage law of Greece, it's probably best if you get in contact with your competent registry office in Greece and ask them about the requirements you need to fulfil, which documents you need to hand in and if there are other things that you need to be aware of. They can give you way more detailed information about the procedure than we are able to.
If you come to the conclusion that this doesn't work for some reason, you can still try to marry in Portugal. As an acknowledged refugee you should have gotten a passport that allows you to travel to most European countries visa free (including Portugal). In this case your fiancé should contact the Portugese registry office and ask them about the procedure.