There is an interview with Mira Furlan's husband from a Croatian magazine which states that Mira Furlan asked to be written out of the show because she didn't like constantly being in Hawaii. Her husband also states that she might be back for the next season.
Why did your wife stop shooting Lost??
"She got bored of Hawaii. She got island fever - that's how cast of Lost calls it in joke. Simply, she didn't want to be on that island, she didn't want to work that job, so she made a deal with the producers to kill her character off."
How did they kill her off?
"Shot her. But, her character is pretty popular with fans of the series, so they leaved possibility for comeback next season."