For some reasons , an organization may like to put an employee salary on hold.

Follow below steps to terminate an employee
1. Create a informational flat rate that salary type of transaction
Follow below screenshot
2. From Employee master , edit the employee for which you need to perform salary on hold
3. Change the transaction head assigned to Salary on Hold
4. Save
5. Remember to change back the salary on hold to the salary head type required when you want the salary to compute
6. If there are any other flat rate earnings , set the value as zero

This will result in payroll for that employee as zero.