There is no clear charter argument to invoke as a public employee. I’ve seen suggestions that a section 7 argument can me made. Maybe. Nothing overly compelling, especially given section 1.

In terms of contractual relationships between a private employer and employee one must also examine statutes and regs in each province as well as any applicable federal laws. In other words the employment contract won’t be the entire story. Moreover, the same doubt regarding the ability to advance a strong charter argument against vaccination under public law would apply under a contractual arrangement, to the extent the charter applies at all.