Unless you have a bug, there's no way to be truly stuck within Ust Natha. The city is sealed by the Matron Mother, who remains in the Temple afterwards. Be sure to try to open doors that were sealed before. Killing her breaks the seal on the main gates, and you can leave.
In case you were wondering, the buildings you can't enter (Deirex's Tower and the House Ja'ellat) have nothing to do with getting out.
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Volothamp's Comeuppance
Everything you ever needed to know about the entire Baldur's Gate series......except spoilers.
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