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Indigo (or for that matter any Indian carrier) offers airport check-in.
Even for web check-in, a lot of seats are available for free - these include the middle seats and those at the back of the plane. You can choose one of them and complete the check-in.
Update: As per revised web check-in policy all seat selections now have an associated fee.
If you don't want to pay for the seat and don't mind being seated anywhere, just go to the airlines counter at airport and they will allot a random seat at check-in. If you are lucky you may get a premium seat for free (Window or aisle and in front of aircraft).