Must money taken as commission be returned to the company owner, or is it permissible to donate it as charity after repentance?

As long as you are an agent for the company owner in awarding bids to suppliers, it is not permissible for you to take any payment from them except with the permission of the employer. If what you take from them is not permissible شرعاً (according to Islamic law), then it is not permissible for you to take it, even if the company owner permits you. You must return what you have taken to them. Neither hardship nor difficulty excuses you from doing what is obligatory.