Wilson has joined Spurs to the end of the season, with the deal including an option to buy.
The 18 year-old striker has scored eight goals in 45 appearances since making his Hearts breakthrough last season but he has struggled for game time this term.
"James wanted to go, so you don't want to keep a player who then becomes unhappy," said McInnes.
"I couldn't guarantee him minutes, such is the way it's been. I told him and his agent that our preference was to stay, fight for his place, be part of something.
"We'd get him a loan in Scotland if need be, to top his minutes up, and we can maybe recall him - still get the best of both worlds.
"But his head was turned with the Tottenham thing. First it was Arsenal, then Arsenal went quiet, and then all of a sudden Tottenham came to the table.
"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.
"I hope it goes well for him because he's a great kid. We'll see how it plays out. I just need to concentrate on the players who are here and who want to be here and play their part."