On the ABC medical drama, Arizona (Jessica Capshaw) recently had her left leg amputated after being severely injured in a plane crash.
"It felt real to me that Arizona would lose her leg," Rhimes wrote on her blog. "To all those of you who posited that Arizona lost a leg because she's a lesbian, I say... we don't punish people for their sexual preferences.
"We allow people, no matter what their sexual preference, to have complex storylines. Arizona is a lesbian who also happens to lose her leg in a plane crash."
Rhimes also insisted that Arizona's new disability would not have a long-term negative impact on her relationship with Callie (Sara Ramirez).
"Callie and Arizona are going to have a fun... sexy love life again," she continued. "And you are going to see it this season.
"That's important to me. I stated in the Writers Room that Arizona could not lose a leg unless we were going to see how a person missing a leg could be sexy."
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The showrunner also praised "fearless" actress Capshaw, who made her Grey's Anatomy debut in 2009.
"It's a pleasure to get to work with someone so game for the story [and] so game for representing things rarely seen on network TV," Rhimes wrote. "I love my job. I love getting to write for her."
Grey's Anatomy airs on Thursdays at 9/8c on ABC. In the UK, the series airs on Sky Living.