We would not be able to delete an agent from Freshservice. If you need to remove the agent from your agent list, you can choose to "Deactivate Agent" profile. This would move the agent to the list of deactivated agents, and the tickets assigned to that particular agent remain assigned to them and you would still be able to run reports on the same.
In order to deactivate an agent profile, please navigate to Admin-->Agents and click on the Agent profile. Now on the far right click on the three dots and choose "Deactivate Agent".
For more information on deactivating agents, please refer to the solution article here.