Gibson told BBC Tees: "It is a big loss but we have to be realistic. I've read comments in the paper that we left it late to start negotiating his contract. That's not true. We started speaking to Mark and his agent last Christmas.
"We made him what we thought was a very good offer. I was told from the onset by his agent that it was all about money, that Mark was for hire and he would go to the highest bidder.
"I found that in the space of a week that bidding had gone up by many millions and it got to a situation where I felt almost tainted by it, it was a really uncomfortable situation.
"I went on behalf of the football club and I spoke to Mark for many hours about it and I took it as far as I was comfortable, in fact I took it to the point where I was uncomfortable, and it was a relief to me when he actually said he was going to Newcastle because of the sums of money that were involved.
"The signings we make are so important to the financial stability of the club because the headline is always the transfer fee but a four or five-year deal with players today can be £15m in wages and maybe £10m in a fee, so your financial risk is £25m and the decisions have to precise, thought about and detailed.
"With Mark Viduka we took it for a player who's 32 next birthday, asking for a three-year contract, asking for a sum of money that would have been per year more than half of the gate income, for one player.
"We looked at the facts and in three years Mark averaged eight goals a season in the Premier League. He turned what I believe to have been a fantastic offer down and we move on."