Big-Dog's opinion notwithstanding, the check cashing store is a holder in due course unless it is aware of the fact that the first check was stopped. That would be the case if the check had already been presented for payment and had been marked "Stop Payment," or if the dishonest employee/payee had boldly claimed that he/she was scamming the boss. But those things didn't happen here. The check-cashing store was ignorant of the sordid details, and cashed the check quite innocently.
The UCC protects the holder in due course and allows it to pursue the issuer of the stopped check.
Annotating the check in an attempt to prevent its being cashed except at a bank wouldn't work, either. The payee's scam could have worked just as well if (s)he had cashed the original check at a bank (other than the bank it's drawn on).
The employer's gripe here is with the former employee. Let's put the blame there, where it belongs. The check-cashing store is entitled to recover for the check. It can pursue the check's payee on his/her endorsement warranty, or it can pursue the employer as the drawer of the check. Which pocket do you think it will pursue, given those options?