Since you have paid due Service Tax along with interest on being pointed out by the Department (Whether pointed out by CERA or Internal Audit of the department, it does not matter),
Extract of Section 73 of the Finance Act, 1994
(3) Where any service tax has not been levied or paid or has been short-levied or short-paid or erroneously refunded, the person chargeable with the service tax, or the person to whom such tax refund has erroneously been made, may pay the amount of such service tax, chargeable or erroneously refunded, on the basis of his own ascertainment thereof, or on the basis of tax ascertained by a Central Excise Officer before service of notice on him under sub-section (1) in respect of such service tax, and inform the [Central Excise Officer] of such payment in writing, who, on receipt of such information shall not serve any notice under sub-section (1) in respect of the amount so paid :
CERA also sends audit report to the department of Central Excise & Service Tax. Hence the department stands informed regarding deposit of ST along with interest
There is a plethora of case laws in your favour. Penalty is not imposable at all. If more information is required, let me know through this forum.