They have temple's to Greek gods because it's a Greek guy telling the story.
If you read Herodotos' History, you'll notice that he even uses the names of Greek gods for Egyptian ones.
(Thot=Hermes, Amon=Zeus, Isis=Demeter etc.)
Just an issue of local versions of the story.
Kritias himself gives an explanation about this:
"Yet, before proceeding further in the narrative, I ought to warn you, that you must not be surprised if you should perhaps hear Hellenic names given to foreigners. I will tell you the reason of this: Solon, who was intending to use the tale for his poem, enquired into the meaning of the names, and found that the early Egyptians in writing them down had translated them into their own language, and he recovered the meaning of the several names and when copying them out again translated them into our language. "
Atlantis waged war on Greek states 900 or 9000 years before Plato writes down his story. I can hardly believe there were real, non mythical Greeks leaders and cities by that time. Even 900 years before Plato still puts this story back as far as the rule of the Egyptian pharaoh Ramses II.
Never is there any mention of the flooding of Atlantis in Plato's dialogue. It just abrubtly ends when he's coming to the interesting part, the thing Zeus has decided to do with Atlantis.
This story is not a Greek myth untill it shows up in Plato's dialogue.
Quote from the translation comes from here:
http://classics.mit.edu/Plato/critias.html
translated by:
Benjamin Jowett