If you are a medical marijuana patient are you protected from a "0" tolerance policy, if the policy was instituted after the patients diagnosis is confirmed. This is a California company

The company will have to be aware of the medical condition and the fact you are on medication that may effect your behavior.

If the use of this ( or other presciptions) would cause an issue with your job, it can be considered.

No you are not protected regardless of the timing. In California, medicinal marijuana users are not covered under the Fair Employment and Housing Act. Even though California law allows medical marijuana for medicinal purposes, it is still considered a Schedule I drug by the DEA (federal). The California medical marijuana law protects you from criminal prosecution, but employment law is considered civil law. California courts have consistently ruled in favor of employers who terminate employers for violating their drug-free policy when the employee/applicant claimed that the marijuana use was for medical purposes.

An important thing to remember here is that employers can terminate you, particularly in California and other at-will states, for things that are legal to do. For example, it's legal to be late to work or to not perform up to standards, but most employers will terminate you for those reasons.

By the way, the location of the headquarters of the employer or the state in which it is incorporated are not relevant, it's where the employee is performing the work. So for example, it may be a California company, but if the employee is based out of Arizona, where the courts have taken the opposite approach to medicinal marijuana use, you would consider where the employee is doing the work. Arizona and one other state (I want to say Rhode Island or Delaware) are the only two states that are considering legislation to protect medical marijuana users from tangible employment action. Everywhere else, like California, you're out of luck.