Dear Querist,
Query-wise reply is as under :-
1. There are two services involved -supply of manpower and construction service (pure labour). Pure labour to Govt. for construction/works contract is exempted but there is no exemption for supply of manpower to any Govt. State or Centre. GST has to be borne by the Contractor and not to be collected from Govt.
There are separate provisions for penalty for each type of offence. If any assessee is required to get registration and he does not get, all penalty will follow for non-registration, non-filing of return and non-payment of tax etc.
2. If contractor is registered for Security Service, he is to follow the procedure and pay GST. If not registered reply given above.
You cannot enter into contract/agreement with Govt. beyond the letter and spirit of GST law.