Is it permissible for an employer to charge an absent employee for the fine incurred due to their absence, given that the fine was for hiring other workers at a higher wage to cover the shortfall?

If the contract does not stipulate a penalty for the delayed worker, then he is not obliged to pay the wages of the (other) workers. The contract is the law between the contracting parties. It is permissible for the employer to deduct an amount for the worker's delay according to the agreement, or the prevailing custom; because what is known by custom is like what is stipulated by Sharia or by condition.