Towering frontman Toni joined Italy's AS Roma on loan until the end of the season after falling out with Bayern coach Louis van Gaal.
"Luca gave FC Bayern great service, but he made the right decision for himself and for us," the team's midfielder Van Bommel was quoted as saying by Sky Sports.
"It would have been difficult with such a player sat on the bench."
Toni's problems with Bayern dominated headlines for several weeks but Van Bommel believes the atmosphere is ideal now for the German giants to deliver.
"The atmosphere is very good. Everybody gets on with everybody else and there is no disturbing influence in there," he added.
Bayern entered the mid-season Bundesliga break in third place with 33 points, two behind leaders Bayer Leverkusen.