Theft By Servant in Kenya: Penalty For Stealing From Employer in Kenya

The company has every right to press charges against you for the theft. As a result of being terminated for theft you will likely also be denied unemployment benefits. Theft is a specific intent crime and is fully committed the moment you move an object with intent to steal it, therefore, offering to give the money back does not change the commission of a crime-it may reduce the penalty the court hands down, though not likely unless it is a first offense.

They employer/company can report the employee to law enforcement authorities for the theft. The fact that the employee offered to pay it back, may or may not have a bearing on whether law enforcement will continue to prosecute the case. Depending upon the amount allegedly taken, the theft could be prosecuted as a misdemeanor or felony. Any employee accused of this, should keep their mouth quiet and immediately seek the advise of a criminal defense attorney (which I am not).

the penalty for stealing from your employer is harsher than stealing forma stranger because it is also a breach of trust. 

You could get anything from a good behaviour bond to a fine. If it was a substantial amount and done over a long period of time you could go to jail. 
How is Embezzlement Punished?
Restitution
Aggravating factors

Embezzlement is one kind of property theft. It occurs when someone who was entrusted to manage or monitor someone else’s money or property steals all or part of that money or property for the taker's personal gain. The key is that the defendant had legal access to another’s money or property, but not legal ownership of it.   Taking the money or property for the defendant’s own gain is stealing; when combined with the fact that this stealing was also a violation of a special position of trust, you have the unique crime of embezzlement.

Embezzlement can occur in a variety of circumstances. For example, a bank teller has legal access to client money, and is trusted to handle but not take that money. Officers and employees of companies can also embezzle funds belonging to the company, as can family members caring for a relative, professionals like lawyers or board members who handle client or investor money, or anyone in a position of trust with regard to someone else’s money or property.

A conviction for embezzlement usually results in a fine, jail or prison time, or both.

The court may require defendants to pay restitution to their victim(s). This usually involves repaying the victim for the monetary value of the money or property embezzled. When applicable, restitution is most often in addition to the applicable fines and prison time.

Many states impose harsher penalties when the defendant embezzled from a specially protected class of victims (such as elderly or disabled adults), or when the defendant had a heightened level of trust with the victim (such as when the defendant is a public servant, or bank or insurance company employee).