Is it permissible to take money from sales without the company's knowledge, in return for the cost of a freelance contract that was not honored?

It is not permissible to take anything from the company's money without its knowledge. The fifty thousand were paid as the price for the employment contract, and you obtained it. If the company terminates the contract after its term expires, you have no right to the fifty thousand. However, if the company terminates the contract before its term, you have no right to what you paid to obtain the contract, because you already obtained it. This is unless the money was paid in exchange for enabling you to work for a specific period, in which case the employee has the right to take his due proportionate to the remaining period. The fundamental principle is the sanctity of another's property, and no one's property becomes lawful for another except with their full consent.