Dear Aniket,
If the policy of your company's CTC states that gratuity is to be part of it, then it has nothing to do with 5 years completion of employees' tenure. It still remains a part of CTC. If, at this moment, based on their request you tend to change it, please keep in mind that it has to be a general change and all other employees about to complete 5 years in the company should also get the benefit, else it may lead to grievances.
The best thing would be to explain to all employees that gratuity as a part of CTC has nothing to do with 5 years. The company is still liable to pay gratuity for "N" number of years they work. I didn't understand the concept of adding gratuity to the gross salary. If it means adding the same amount of contribution under some other head in the gross salary, they are pointing towards an increment. In such a case, ideally you should not do so and introduce a commitment bonus, the amount of which can be decided by your management (e.g., Rs. 1000 * number of service years completed above 5 years. The amount can vary depending on the grade of the employee). This will motivate them and also give them the feeling of being recognized in the company.
Secondly, as Ms. Avika said, if the company is liable to pay to show gratitude and it should not be considered as part of CTC, then it must be from day one. Gratitude doesn't come in only after 5 years. This would further demotivate your employees who have not completed 5 years.
Please look into several other factors before bringing in the amendment. You must also understand that the management should be ready to accept this huge liability.
Regards,
Hiral