Can I be disciplined for reflecting/praying at my desk quietly?

It depends on the circumstances. Unless you work for the govenment (e.g. school district, government agency, military) or a institution which is largely government funded (e.g. many universities), the First Amendment and it protection of religions expression does not apply to you. That said, an employer may not discriminate against someone on the basis of religion.  However, the employer has a fair amount of latitude to regulate actual behavior in the workplace. So while you cannot be disciplined because you are a person of faith, if you are, for example, praying while you should be working (i.e. taking time to pray is affecting your workplace performance or causing you be insubordinate in some fashion), the employer probably could take action. So the answer will likely turn on whether the action is being taken because you are religious, or it's occuring because you are doing something negatively affecting your own job or the workplace. Since the facts are so important, you should consult with an emloyment law attorney to evaluate the situation.