I usually feel like that for most unnatural deaths. I try to justify by creating a narrative and a greater purpose as to why I had to kill them.
Example: Before they fixed the "townies don't change clothes or age" glitch when you moved them into the household, I had killed two sims on different occasions because I wanted them not to be alive on my sim's family tree. They both starved to death. To justify it, I pretended they went on a hunger strike to protest the fact they couldn't change clothes and had rejected immortality.
All my sims usually die of old age, but every once in awhile I'll tempt fate, like keeping sims I am not attached to hysterical, enraged, or fixing an electric item in a puddle of water. Hey...got to have life be a little unpredictable. I don't feel guilty when I do this because accidents happen no matter how perfect life may be. It also helps my remaining sims to open up new game play.
Don't feel bad. Cow plants have to eat too! Plus, I'm sure if they had one, a Cow Plant's lifetime aspiration would be to produce the milk "essence of life". So in a way, you've made your cow plant very happy!
Don't they get the "feels like an emotionless shell" moodlet when they get spit out the first time? Maybe she didn't want to live anymore and decided to donate her essence so that Phoebe can drink it and live a long life with their child. Maybe that's why you didn't feel connected to her; she had a greater purpose.
Edit: Grammar