Such a small number of Greek tragedies survive that it is difficult to speak with any confidence of their conventions, but it seems to have been the case that the action of the play never took place in Athens. The terrible events were always located in some conveniently distant place: Troy, Aulis, Tauris, Thebes, or, as in Medea, Corinth. Athens was therefore able to be a city of safety and reason, untouched by pollution.

It is ironic, therefore, that it is one of the most tragic figures in the history of Athens, the mythical King Aegeus, who allows Medea safe passage to Athens shortly before the chorus sings its third ode. The ode offers an implicit contrast between the chaos of Corinthian politics, which is soon to erupt into murder and infanticide, and the calm of Athens, the "holy country, never conquered, never ransacked by its enemies." The people of Athens are happy and wise, says the chorus. There, Aphrodite sends Love to sit beside Wisdom "to foster all fine things."

This praise is apposite because Aegeus has just promised Medea sanctuary in Athens and because the play is being performed before an audience of Athenians. Its final purpose, however, is stated at the end of the ode itself when the chorus asks Medea:

How will this city of sacred streams,
this land of strolling lovers,
welcome you—a murderess
who slaughtered her own children,
an unholy woman—among its people?

The chorus pleads with Medea to relent and spare her children, since she will bring pollution upon the glory of Athens as well as on herself by shedding their blood.

All quotations are from Ian Johnston's translation of Medea, linked below.

I don't see the Chorus' praising of Athens as something in the form of nationalism or political zeal.  Their praise of Athens is more of a validation of how moderation and a sense of control must exist within people of a community in order for a community to function and prosper.  Their praise of Athens presents Euripides with another path to show how people wronged can pursue their own feelings of anger and resentment.  Athens is shown to be a source of wisdom, judgment, and grace.  The Chorus praises Athens precisely because Medea's plans to murder her children represent the exact opposite. 

The Chorus operates in this moderate vein.  They are the force that  supports Medea as a woman, but distances themselves from what she does. The Chorus is very quick to criticize Jason and support Medea for feeling wronged.  Yet, when the Chorus speaks out against Medea's vengeance that embraces the killing of her children, the Chorus cannot support such action.  When the Chorus hears of her children being killed, the Chorus speaks out against what is happening:

She fell, poor woman, into the sea, in an
impious murder of her children,
stepping too far on the promontory,
and she perished, dying with her two sons.
After this, is anything too horrible to happen?
O bed of women, site of many labors,
how many evils you have already
brought to humanity.

The Chorus operates as a force that speaks to vengeance as being something that cannot be tolerated in a civil society.  The Chorus of Women praises Athens because the vision of social progress and elevated thought that it represents is superior to the base and savage instincts that Medea embodies.  In their praise of Athens, the Chorus, while supporting Medea's anger, seeks to raise her condition from one seen as an animal to something more of a human.  The Chorus praises Athens, invoking it as a potential for what can be, as opposed to Medea who embodies more of what sadly is for human beings.