Conor Berry resigned after incorrectly tweeting that the suspect wore Trump-branded clothing.
The president has previously used the phrase "enemy of the people" to describe the media.
Dana Loesch denied she was referring to journalists when she made the comment and claimed she was talking about inaccurate stories.
Thomas Marquardt said the paper wasn't sure how to handle Jarrod Ramos and considered getting a restraining order against him.
"I'm going to need more than a couple days of news coverage and some thoughts and prayers," Capital Gazette staff writer Selene San Felice said.