Regarding your questions, the first answer is that it is correct that the body transcendental of Krsna and Krsna Himself are nondifferent. So what is the difficulty to understand that the soul of Aghasura merged into the body of Krsna? In other words Krsna benedicts the demons Whom He kills personally with the impersonal liberation of merging with Him.
There is a difference between the activities of Krsna which are exhibited to the perception of the conditioned souls in this world and His activities in Goloka Vrndavana. Because Krsna was playing as an ordinary human being, His activities here appear just like ordinary human activities, but in the Spiritual Sky there is no such requirement. There in the spiritual sky Krsna has His activities also but they cannot be understood by the conditioned living entities how they are going on without any resemblance of the mechanical workings of things in this material world.