As far as I know, Indra and Vritra came to an agreement after the war and became friends. Then why did Indra kill Vritra? And why did Bhagwan Vishnu help him? Did Vritra commit any sinful act?
Section X of Udyoga Parva of Mahabharata has a version of this story.
According to that, it was Vishu only who suggested Rishis and Gandharvas to propose peace offering between Indra and Vritra.
And Vishnu said, 'I am no doubt bound to do what is for your good. I shall, therefore, tell you of a contrivance whereby he may be annihilated. Do ye with the Rishis and the Gandharvas repair to the place where Vritra that bearer of a universal form is and adopt towards him a conciliatory policy. You will thus succeed in overthrowing him.
Vishu says he is bound to do whatever is good for devas, Indra.
But this friendship/peace offering was to buy time and opportunity for Indra to kill Vritra as you may see from above passage.
Thus peace having been concluded, Vritra was very much pleased. And Indra also became pleased though constantly occupied with the thought of killing Vritra. And the chief of the deities passed his time in search of a loophole, uneasy (in mind). And on a certain day when it was evening and the hour awful, Indra caught sight of the mighty Asura on the coast of the sea. And he bethought himself of the boon that was granted to the illustrious Asura, saying, 'This is the awful evening time; it is neither day, nor night; and this Vritra, my enemy, who hath stripped me of my all, must undoubtedly be killed by me. If I do not kill Vritra, this great and mighty Asura of gigantic frame, even by deceit, it will not go well with me.'
As you can see, even after friendship, Indra still thinks of Vritra as enemy. He has constant fear that Vritra will not do good to him. Eventually the plan was to kill Vritra.