agreement for sale

In which state the property is situated? the stamp duty varies from one state to one state.

1. the property can be directly transferred to the second purchaser without executing the sale deed on the name of the first purchaser,

2. an intense look on the agreement to sell is required

The stamp duty shall be apllicable as of the date on which sale deed is made, forget about the agreement date. Sale deed shall attarct full stamp duty and other fee /charges  as  effective in the place as on the date of sale deed

From your querry I am of the opinion that the sale agreement is registered between seller and buyer and still the sale is pending.  If the sale agreement holder wants to register the property in other persons favour the same can be registered in his/her favour on the same day or later within the limitation period.  Registration charges paid will be considered (deducted) for payment of final sum.

Sale transaction is incomplete and the property is yet to be transferred in the name of purchaser. Stamp duty paid for registration of "agreement" to sell can not be refunded.

The seller may sell to someone else and get the transaction directly with new vendee. 

It is advisable to consult a local prudent lawyer for appreciation of facts/ documents, professional guidance and proceeding if required.