It sounds like you are saying the top manager is stating the employee was not following methods, then saying the employee was dishonest. It's not really clear what you mean. If the Manager stated the employee was not following methods and the employee disagreed, which led to the Manager stating the employee was lying, the employee needs to ask for documented proof or examples of how s/he was not following methods.
If the employee is just being accused of being dishonest, s/he needs to let that roll of her/his back rather than lose the job. People get accused of all kinds of things, but if the employee is known as a person of integrity by other employees, and by her/his own conscience, stand firm. It's not worth making mountains out of molehills because jobs are hard to find, hard to keep in this economy, and there will be issues everywhere.
The Lord will fight for His kids. I've experienced it.