Sandya is kept alive by GS not because she is the heroine but they need to get the information about what all the secrets she has already shared with her team, so that they can make alternative plans. Otherwise they can't go ahead with their original plan if the Govt has already prepared for the same with counter plan. If they had to kill her, they could have killed her the day they caught her and there was absolutely no need fro them to keep her alive till now.
Even for Police, there was no need for them to risk if they had planned only to kill one or 2 people. They had to get hold of the secret plans of the GS so that they can fail their attempt as well as eradicate them.