Generally, under California Labor law, a prospective employer can ask you about criminal convictions and about open arrests. If you were arrested for Penal Code Section 69, it means that, until your case has been rejected, it is an open felony arrest. So, if you filled out your application before the case was rejected by the prosecutor, you probably were required to disclose it.
The fact that a case was not filed by the time of the arraignment does not mean that it has been rejected. Quite often cases are filed after the arraignment date and the person is sent a letter to appear. (So, make sure that the address that the police have for you is current and that you are getting your mail there.)
Employers can fire a person for lying on their employment application. So, if you filed a false application, then it would be a supportable ground for firing.
Now, if the case was actually rejected at the time you filled out your application, then firing you for not disclosing an arrest that is not open and that did not result in conviction would be wrongful. You might well have grounds for reinstatement or even a cause of action for wronfgful termination. You should talk to an employment lawyer about this right away. The lawyer can determine if you were discharged in violation of public policy and whether that constitutes adequate grounds for asserting a claim.
Having said all of that, of course, your lawyer will want to know what emploment you had applied for. If it involved a security clearance or other federal requirements, then the state Labor Code would be superseded by federal regualtions. And, of course, an employer could chose not to hire you because of conduct of which they became aware, e.g., from postings on Facebook or local news stories indicating that you had been involved in conduct of which they did not approve. But, if you were actually hired and then fired for not disclosing something that the law protects you from disclosing, you may have a good position. Talk to the employment lawyer.
Finally, if the PC Section 69 case is pending review in the DA's Office, you should really hire the best criminal defense lawyer you can find. She or he can try to intercede before a filing decision is made or, at least, start investigating the case to defend you. You definitely do not want to face felony charges or end up with a felony conviction if you can avoid it. Talk to the criminal defense lawyer about all of this.
The answer to your question depends on when the background check was performed and what the status of your criminal charges were at the time they were performed. It is illegal for an employer to make employment decisions (hiring, firing, etc.) based on arrests alone. See Cal. Labor Code 432.7. However, nothing in that section shall prevent an employer from asking an employee or applicant for employment about an arrest for which the employee or applicant is out on bail or on his or her own recognizance pending trial.
Nothing in this section shall prevent an employer from asking an employee or applicant for employment about an arrest for which the employee or applicant is out on bail or on his or her own recognizance pending trial.