1) I hear that a sub- lease aggreement registration between B and C is not possible legally since there is already an agreement between A and B.
Actually if there is an agreement between church and A, then if the provision permits A to sub lease the same B, then the sub sub lease agreement also can be executed.
2) By written permisson of A, you mean just a letter or an aggreement that is not registered ?
Actually it can be termed as sub-letting by the sub lessor.
This is an agreement to sublet real property according to the terms
The sublessor agrees to sublet and the subtenant agrees to take the premises. Both
parties agree to keep, perform and fulfill the promises, conditions and agreements
3) Incase, on a mutual understanding, an aggreement is formed between B and C, and notarized saying the land is taken on sublease therein the shed in the land is also leased for 5 years, would it be legally valid incase of dispute in the future ?
The B being sub lessor, can sub let the shed on an agreement and the C will be the sub tenant.
Therefore you may proceed with the proposed sub tenancy by drawing a sub tenancy agreement deed.