I don't really think the babies deserved it(having not even been to the shop), but if they can't tell that they're eating their sibling then killing them is just clearing the gene pool.
No, that's not the missing koMarisa. Anon put the hat on the half-eaten doughnut and the babies recognized it as their big sister, whom they had been "eating".
Accessories seem to play a big part in this story, and seeing as the donuts are made out of yukkuris, it does seem as if he just put the hat on the donut.
Yukkuri's identification uses simplified version of duck testing: if it has a Yukkuri/Anon accesory, then it is that Yukkuri/Anon. As an example, Papa Marisa thought it was killing YunDonutsAnon and actually was Mama Reimu with YunDonutsAnon cap.
No, after more consideration, I think it's actually a donut. This koMarisa has her right eye intact; the real one had hers removed by anon and fed to it.