What is the ruling of Sharia on an employee taking some goods (vegetables and fruits) from their workplace without clear permission from the employer, even if the employer is aware of it, and is what the questioner did by paying the value of these goods to the company considered a way to absolve himself of sin?

The fundamental principle is that it is forbidden to take people's money without their consent. If the actions of these individuals are based on their knowledge of the owner's consent, derived from strong circumstantial evidence, then there is no harm. However, mere silence after gaining knowledge is not sufficient, as shyness might prevent some people from objecting. The employer's consent for the store manager to take items for himself does not imply permission for him to give them to others. Therefore, your taking of goods without certainty that the man is authorized to give them to people necessitates repentance and the return of an equivalent if what was taken is from fungible items (measurable by volume, weight, or count), or the return of the value if it is from non-fungible items (that which cannot be measured by volume, weight, or count). If what you took was non-fungible and you paid its value, then you have cleared your conscience. If it was fungible, then you must return its equivalent. You can seek a way to recover what you paid in value. If it is possible to be forthright with the rightful owner and he agrees to accept the value you returned, then your conscience is cleared thereby.