I don't think we actually know if she did choose Yamato. I think Michuru confessing to Yamato earlier on in the story during her last moments was more of a tactical decision on the character's part to give Yamato the necessary motivation to change the future. Whether or not those were her true...
Even in the LN, chapter 82 2nd volume, the 3rd evolution was translated as the "Evil Plague Dragon" so I can understand why it's called like this here.
Calamity Dragon does sound cooler though