The 18-year-old completed a loan switch to Spurs on transfer deadline day on Monday. He joins their Premier League 2 side, where he will try to earn a permanent deal.
A fee of around £2.5million has been agreed between the two clubs, should Spurs want to take up the option in the summer.
Wilson was keen on a move in the window.
He had been limited to just 10 appearances this season after an impressive pre-season and Premier Sports Cup group stage campaign, starting three of the four games and scoring twice. He then fell behind Claudio Braga and Landry Kabore in the pecking order, starting just one league game.
While understanding of the teenager's position, McInnes wanted Wilson to stay and even go out on loan in Scotland with a view to being recalled.
"James wanted to go, that has to be said. So you don't want to keep a player who then becomes unhappy. I couldn't guarantee him minutes, such as the way it's been," he said.
"I told him, his agent knew that our preference was to stay, fight for your place, be part of something, get you a loan in Scotland if need be, if you need to top your minutes up and we can maybe recall you. So you still get the best of both worlds."
Deadline day saw Arsenal and Spurs competing for Wilson's signature, with the latter winning out in the transfer tussle.
McInnes believes he is better than playing Premier League 2.
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"His head was turned with the Tottenham thing. First of all, it was Arsenal, then Arsenal went quiet and then all of a sudden Tottenham came to the table [Monday afternoon]," he said.
"I don't think it's the right move for him. Ultimately, it's academy football and I think he's better than that. But it was something James wanted to do.
"So, like I say, we made it clear that our preference was for him to stay and be part of something here. But he made the decision and I hope it goes well for him because he's a great kid and we'll see how it plays out.
"But for us, I just need to concentrate on the players who are here and who want to be here and who want to play their part."