McInnes told the Bristol Evening Post: "I can understand the frustration and anxiety among the supporters. There is a lot of emotion in football and that is why we all love the game - but I think Nicky is quite within his rights to see out his contract if that is what he wants to do.
"We still want him to commit to a long-term contract and he has told us he does not want to do that at the moment. That means we have to look after the interests of the football club and try and get back some of the money invested in him.
"I'm disappointed by his decision, but I respect it at the same time.
"Now is the time to draw a line under the whole hullabaloo and move forward."