How can one get rid of the consequences of secretly taking money from an employer, while repenting and being unable to repay the amount?

Congratulations on your repentance and remorse for what you have done. For whoever repents, Allah accepts his repentance. One of the conditions for repentance is to exert effort to return the money taken unjustly to its owner, estimating it as accurately as possible so that it does not increase, and then returning it by any possible means. The inability to pay the debt does not prevent repentance, but it remains a debt upon you that you fulfill to the best of your ability. If you can inform the shop owner and seek his forgiveness, do so to clear your conscience.