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The simplest solution is, after the marriage has taken place, is to go to the Italian Immigration office (or local Anagrafe) and apply for an Article 10 residence card (Family member of a Union citizen). Italy, as apposed to some other EU countries, will issue a Article 10 card to the spouse of an Italian citizen.
DIRECTIVE 2004/38/EC OF THE EUROPEAN ...
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You can absolutely leave safely. The problems may occur when she returns. As mentioned in the other answer - if you both intend to live in Italy, the simplest solution would be to apply for the Italian residence permit before leaving. While there may be a potential fine assessed during that application (maybe? probably? unlikely? Who knows...), the residence ...
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As the spouse of an Italian citizen, your wife will benefit from freedom of movement rights when traveling with you (or to join you), so no ban will be possible. It's very unlikely that an officer would try to impose a fine relating to an overstay before the marriage (if such a fine would even be lawful),
I don't have much experience with Portuguese border ...
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