The Daily Wire even headlined their story: "Debra Messing Issues Homophobic Insult To Trump: 'I Hope' You Become 'Most Popular Boyfriend' In Prison."
The article sparked a fierce reaction from the actress on Monday, who insisted she was an ally of the LGBTQ community.
"Let me be clear: I said nothing about LGBTQI/queer LOVE," Messing responded.
"Rape is an act of violence. Trump has perpetrated violence on hundreds of millions of people. My hope is (and this is the first time in my life) that the tables are turned and he is the victim of perpetrators. #LGBTQIAally"
Her follow-up tweet, which has also been deleted, drew more condemnation.
"So, to be 'clear,' she's not using a somewhat flippant prison-boyfriend expression to indicate her disdain for the president, she literally wants him to be raped! Well, ok, that clears things up," journalist Jeryl Bier reacted.
"There are so many actors, actress, musicians, etc. that I used to like and would continue to like had they never signed up for Twitter. Perhaps not all thoughts need to be blasted out to millions," Manhattan Institute senior fellow Brian Riedl wrote.
"This is DISGUSTING. might be the most heinous thing i've seen on twitter. prison rape is a huge problem, not an issue to be taken lightly or wished upon a political enemy," The Blaze's Jessica O'Donnell reacted.
"I've been in this situation at dinner parties where everyone just stares at you blankly after you're like, 'Oh no no no you misunderstood me. I was just saying, I think he needs to be violently prison raped. Is that better?'" comic Robby Slowik tweeted.
The actress tweeted once more to make her stance known, writing: "I'd like to say I have been an LGBTQIA ally for decades, and I was in no way referencing LGBTQI/queer love/sexuality. It is not my proudest moment, but 45 has victimized 100s of millions of ppl; I had wished the tables turned on him. I apologize for the offensive way I did it (sic)."
A number of followers flocked to defend her, with one writing: "Most of us have done this sort of thing. I know I have. It just doesn't become a story when I do. Handling it this gracefully is admirable."
Another said: "No apology necessary for me, personally. The 'Will & Grace' effect started making waves and gave me the courage to come out in high school in middle Tennessee in 2001. You're a trailblazer who made some of our lives possible as they are. Apology demanders, learn your history!!!"
One more wrote: "I knew what you meant. Only those that want drama cause drama. You are OK, lady. Be kinder to yourself. Tell yourself what you would say to a friend who was in the same situation."
Messing and Mr Trump have long been social media enemies.
Back in 2019, Trump referred to Messing as a "McCarthy style Racist" after #RacistDebraMessing began trending following the star liking a Baptist church's sign that called black Trump voters "mentally ill" and white votes for the president "pure racism".
Messing apologised for liking the post, but Mr Trump called for her to be fired from Will & Grace.
"Bad 'actress' Debra The Mess Messing is in hot water," Mr Trump tweeted.
"She wants to create a 'Blacklist' of Trump supporters, & is being accused of McCarthyism. Is also being accused of being a Racist because of the terrible things she said about blacks and mental illness.
"If Roseanne Barr said what she did, even being on a much higher rated show, she would have been thrown off television. Will Fake News NBC allow a McCarthy style Racist to continue? ABC fired Roseanne. Watch the double standard!"
Roseanne Barr's show Roseanne was cancelled in 2018 by ABC after she made racist comments about a former adviser to President Obama, Valerie Jarrett.