How can one absolve oneself of responsibility for an embezzled amount without informing the company owners, by merely waiving the equivalent legal compensation, and what if they insist on compensation?

What you did by embezzling is forbidden, and you must repent from it and return the money to its owners. If the company owes you money equal to what you took from it, then your relinquishing that debt to the company is sufficient. Otherwise, you must return the money to the company by any possible means, concealing your name if necessary.