The reason why Shivji punished Naageshwari has more to do with her killing an innocent man "Akesh" I think Akesh in previous birth was a misunderstood person, He was evil like Veer was in the beginning as well but at the sametime he was innocent and not a horrible person who deserve death.
We can see how Jay is being punished and his power is reduced for killing an innocent man, It's the same that happened to Naageshwari even though her intentions wasn't wrong at all then.