Is the company's money permissible, considering that it borrows with usury to pay employees' salaries, and must the questioner leave working for it?

Borrowing from a bank with interest is religiously forbidden because it is usury (riba). It is not permissible for a company to borrow from usurious banks to pay salaries or for any other purpose. There is no sin upon the workers for receiving their salaries from the company, because its money is mixed, and the prohibition of a usurious loan pertains to the liability of the borrower, not to the money itself. There is no objection to you remaining in the company, provided that you do not engage in any forbidden work within it.