A video first leaked Saturday contained derogatory references to homosexuals and was filled with profanity.
In another scene, male sailors dressed in drag mimic masturbation. In another, sailors simulate a rectal exam.
Clark described Honors as an outstanding officer with a tremendous record of accomplishment. He said that it's very difficult for those who were offended by the videos to speak up, especially if they are at a lower rank than Honors.
"They can't speak up easily for themselves in a senior subordinate relationship and yet they do have feelings, you've got to respect that," Clark said.
Calling the videos "inappropriate," a spokesman for the Navy's Fleet Force Command said in a statement that "the Navy does not endorse or condone these kinds of actions."
Navy officials are deciding whether the videos are evidence of official misconduct or grounds to keep Honors from the helm of the Enterprise for good.
"If it were a younger enlisted sailor that would be one thing, but he's a Navy captain, he is a significant figure in the United States Navy," Col. Stephen Ganyard said.
The Navy clearly spells out the behavior expected of all officers in its code of conduct, which includes such rules as "abide by an uncompromising code of integrity" and "exhibit the highest degree of moral character."
Since the videos were first revealed to the public, several sailors defended Honors on the Enterprise's Facebook page.
"I served on Enterprise for the last three years of my 21-year Navy career. I would love to go to sea with a man like this that can lighten up a extremely stressful job," wrote one, Gordon Wilcox.
"We all looked forward to those videos from Honors while under way. We cannot ruin a good man's career for the sake of petty political correctness," wrote another, Shaun Valentine.
"I, too, was on that deployment. Capt. Honors brought up our morale and provided well-needed and appreciated comic relief. We were under way for long durations, supporting two theaters of war simultaneously, he brought many smiles to a worn out ans tired crew. I can easily say that all of the crew, ship's company & air wing embarked, appreciated the videos," wrote Chief Petty Officer Andrew Hodyl.
Some suggested there was more to the story than the clips that were leaked to the press.
"The clips being shown on the news are out of context and edited to look vulgar," Melissa Nielson posted, calling the reporting a "witch hunt."
"Where are the inspirational messages to the crew that were aired?" she asked.
Several posters had changed their Facebook profile pictures to Captain Owens' official Navy photograph.
Wes Stooksbury, one of those who changed their photos, wrote, "To whichever 'loyal' crewmember has betrayed your captain: It's stunts like that that make me wish the days of corporal punishment were still around. You need to be keel-hauled. Shame on you for potentially destroying at least one great man's career, possibly two now that they have opened an investigation into Admiral [Larry] Rice's involvement. But, alas, you hid behind anonymity like the coward you are."
Not everyone on the page defended Capt. Honors' behavior.
"A laugh shouldn't come from such offensive material especially from such a high-ranking officer," wrote Benjamin Daniel Jenkins, whose comment received many angry replies from Honors' supporters.
Other retired military officials disagreed with Honors' videos, regardless of the context.
"I'll laugh along with South Park along with everyone else, but that's not his job. He's the senior leadership on that ship. He sets the tone of what is appropriate and what is not. You can bring comedians on the ship and that is good for morale, but that's not his role on this ship," retired Marine Corps Col. Steve Ganyard, a former F-18 pilot who commanded an Air Group, told ABC News.