The 30-year-old, who had been with the Dons since January 2014 and had scored 88 goals in all competitions, joined the National League outfit for an undisclosed fee on Thursday.
McInnes described Rooney's exit as "disappointing", but concedes that Aberdeen will have to deal with it and try to bring in new players throughout the transfer window.
"The first conversation I had about Adam was on the first day of pre-season and let's say they were given no encouragement," McInnes told Sky Sports News. "But they have certainly showed an ambition to get Adam.
"It is a challenge for us to retain our players a lot of the time. We have lost out on players to League One which I think a club like Aberdeen shouldn't be. For me I see the levels, I understand the Championship trying to match the Premiership in England and what other teams can provide.
"There is no criticism about it. I understand, Adam has given me some of reasons as to why he wants to go and Salford are certainly a team in a hurry to do well. It's disappointing for us none the less but we deal with it and we concentrate now on trying to get players in."
Aberdeen face West Bromwich Albion on Friday at Pittodrie in a pre-season friendly.