Hong slammed the handling of the row, which erupted after Park Jong-woo held up a sign referring to a territorial dispute between South Korea and Japan.
The incident happened after South Korea had beaten Japan 2-0 in the bronze medal game in London earlier this month, prompting Olympic officials to ban Park from the podium.
"He was as big a contributor to the team as anyone," Hong told a news conference in Seoul. "As far as I am concerned, he is a well-deserving bronze medallist.
"That should have been his moment to remember, and he never got that chance."
The placard - which read "Dokdo is our territory" - helped inflame fresh controversy after a surprise visit by South Korean President Lee Myung-bak to the island two weeks ago.
Soccer's governing body, FIFA, also opened disciplinary proceedings against the player, who was passed the sign by a fan from the stands and has yet to get his bronze medal.
The Korean Olympic Committee (KOC) asked Park not to attend official banquets or functions to celebrate South Korea's first Olympic soccer medal.
"When I heard the KOC decided not to let Park attend these events, I was very disappointed," said Hong, who captained South Korea to the semi-finals of the 2002 World Cup.
"I personally called him and told him to come. It was the least I could do as his coach."
The Korea Football Association (KFA) has come under fire at home for writing to their counterparts in Japan stressing Park's headline-grabbing stunt was not premeditated.
The country's National Assembly weighed in on the issue, Yonhap news agency reported, with the KFA perceived by some as being soft by writing to Japan.
The KFA denied the document was an apology, merely clarification of Park's "impulsive" act and expressed "hope the two sides will be able to work together to prevent similar incidents in the future."
Hong, tipped as a future coach of the national side, criticised the decision to write the letter at all, saying the KFA "should have been more careful."
The disputed islands, controlled by South Korea but also claimed by Japan, lie equidistant from the two countries and are believed to contain frozen natural gas deposits potentially worth billions.