Is it permissible to work in a slaughterhouse that contains pork and beef in order to obtain a commercial license for two years without pay, knowing that the salary comes from another source?

If you are able to limit your work to that which pertains to cows, and their slaughter is done in a Shariah-compliant manner, then there is no objection to you working in this slaughterhouse. Otherwise, it is not permissible for you to work there.