Why? Because Miller's primary motive was to break Rho whichever way he could. He recognised Rho had been trained to or was, by his nature, able to withstand normal interrogation techniques.
Miller wanted to see if he could use kindness or at least appeal to other needs Rho had. Once Rho had submitted, Miller knew he had "broken" him and the experiment was over. Underlying that was a fatalistic recognition that Rho had no future. Miller had already prevented his execution once (probably by a gunshot to the head while bound and hooded never seeing or experiencing freedom or sunshine again). The usual fate of prisoners who were no longer needed. To Miller, at least Rho found peace and did not die in fear.
Let's look at the other interpretation. Rho never saw a "positive outcome" coming. Could Miller have gone AWOL and kept Rho at his farm?
Possibly, but why have that sentence in there at all? Remember we are in Rho's head at this point in time. Wouldn't the verb have been "happening"? and why place this at the end of the story. It's an omniscient viewpoint and would more likely have occurred earlier before we are shown how "good" it is. In fact, the story could have simply ended with "And it's good.
Personally, I felt the tragic ending suited the situation even though I felt gutted after.
But I could picture Miller doing it almost out of kindness and Rho's death would haunt him ever after. Where could he go from there? Could he ever redeem himself or would he see his soul forever tainted with that stain?"