Is it permissible for me to take a commission from a software company in exchange for marketing its products to another company, knowing that I am their marketing agent and the price does not differ whether I take the commission or not?

If accompanying the manager is part of the work, then it is not permissible to take a commission unless the company gives permission. However, if it is not part of the work and the departure was with the permission of an authorized person, then there is no harm in taking the commission. But if the departure was in violation of company policy and without valid permission, then you have fallen short in your work, and the company has the right to deduct a portion of your salary or take the entire commission, unless they grant you permission for it.