I don't think he changed that much, maybe he was just starting to get past his best physically but doe me really it was a combination of not adapting to a new environment well(partly due to injury), a great performance by Gonzaga and perhaps a decline in motivation. You look at his UFC debut for example and I think he still looks quick and sharp vs Sanchez but ends up chasing him too much in the larger octagon.
We saw prime Mirko KOed by Randleman and for me that Gonzaga fight is similar, it basically needed Gabe to fight the perfect fight and finish inside of a round to win. Generally I think Mirko's style was always a high risk one, a lot of the better MMA strikers actually spend most of the fight picking away from the outside but he hardly ever did that, almost everything he threw was potentially fight ending(a lot of it counters) and that ment he put himself in harms way a lot.
Post Gonzaga is when the decline set in, vs Kongo I think lack of adaptation to the cage and Cheiks cheating were clearly issues as well but by the time of his second UFC run he was clearly not the same fighter at all. Watch the fights vs Sanchez and then Al Turk and its clear Mirko has slowed down a ton in a couple of years as the injuries piled up.