He is rightfully controversial, I think the SEALs were hurt by him and that they have been recovering for years from his influence on their culture and that they have improved because of their learning from Army Special Operations culture and experience in recent decades.
Hurt in what way and by what actions?
Lt. Cmdr. Michael J. Walsh, Seal and Vietnam vet, wrote about his run in with Marcinko in his autobiography, "SEAL!: From Vietnam's PHOENIX Program to Central America's Drug Wars". TLDR, he thought Marcinko was unprofessional, more than a little crazy, power mad, and wanted nothing to do with him.
Dale Andrade wrote a series of articles in "Soldier of Fortune" about Marcinko and Red Cell. While the U.S. military and Navy have issues with security during the 1980s, when the Navy let Marcinko create Red Cell to test security went out of his way to take the mission too far. During one Red Cell exercise, Marcinko took a civilian contractor named Ronald D. Sheridan off base, gave him a "mock interrogation" for 30 hours and hospitalized him. He deliberately beat up a civilian to get back at him. To Red Cell, humiliating people and getting away with it was more important then testing and fixing security issues. (1), (2).
After Sheridan sued Marcinko and the Navy, Marcinko was willing to sell out everyone around him to save himself. (3)
Naturally, when Marcinko got out of prison and reinvented himself as the ultimate soldier, a management and leadership guru, he left all the damage he caused in his wake out of it.