It is obvious to me that your future spouse was using a tourist visa for living and working in Moscow, especially giving the fact that she worked in Moscow without authorization " She has lived in Moscow for the last six years staying on a tourist visa and returning every 90 days to Moldova for a short visit before returning to Moscow". You stated that yourself " she does not the have legal right to do so."
For a Moldova citizen's visa processing logically should be done the US Consulate in Chisinau. I think your fiancée will have hard time explaining why she did not seek any legal right to work in Moscow without a legitimate "propiska (lawful residence permit passport stamp), required work authorization or registration as a Russian Permanent Resident and why she kept on travelling there as a tourist yet, living and working there permanently.
In my opinion, these issues may be construed as not following the administrative law of Russia by a Moldova citizen in the eyes of the U.S. Consular Visa Section.
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Immigrant and fiancee visa interviews are handled at the country of residence. You are in a tough spot since she will not be able to show residence in Russia based on your facts. On the other hand, it is not necessarily relevant since NVC will ultimately decide which consulate should have jurisdiction over K1 visa application of a Moldovan national. Chances are you will have the processing done in Moldova although, if she wants to, she can ask the process to happen in Moscow.
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