If I remember right, it was because he had to pick up a package of meth that was at Jesse's and Jesse was responsible for it... but he was out cold with Jane.
Walt made the choice he did in that moment out of anger and disgust at Jesse. "How could he risk the thing I built?"
Her and Jesse were planning on leaving, walt knew if they left with all of Jesse's money they would have shot it all up in their arms and overdosed anyways or ran of money quickly. Walt let her die, cause in his mind he was saving Jesse and this was gonna happen eventually anyways.