Note that per the comment privilege page, comments are "temporary 'Post-It' notes left on a question or answer." The very nature of comments are to be transient clarifications or constructive feedbacks1. Once the comment has served its purpose (ie: the feedback/criticism has been taken into account or decided not to be acted on), the comment no longer has any purpose.
If you truly believe that a comment is "so valuable that [it] deserve[s] to stay indefinitely," then that comment should either be edited into the question/answer or made an answer in its own right!
In that light, let's take a look at the comment you left. It read:
Only your first two paragraphs are responding to the question. I see no difference between "educating" and "making aware". The rest is a rant about the new Code of Conduct and off topic. I agree that it was rolled out abysmally, but I also agree with its aim of treating people with respect and allowing them to be comfortable participating on all SE sites. I didn't mention the CoC at all, and we should all be promoting respect anyway, not just because some lawyer speak CoC tells us to. So, can you answer the question in line with the spirit of the CoC, i.e. treating everyone with respect? — Cool Fool 2 mins ago
As others have said, if you want your question to be answered in a certain way that you find answers are not addressing, that usually means that your question needs to be edited. But even disregarding that and the way this can be read, it looks like in the end, you're making a request of the answerer.
If I were the answerer and I am given feedback I choose not to act on, then the comment has served its purpose. I'd flag it as "No Longer Needed," since I'm choosing not to act on that advice. It sounds like OP did something similar in this case.
If I were the commenter and I saw my comment had been deleted (in other words, my advice is not going to be taken) and I felt the answer was still not up to snuff given my question, I'd flag the answer as "Not an Answer," which will throw it into the queue and let the community decide whether or not it actually answers my question.
TL;DR/Conclusion: At the end of the day though, you can't simply make demands of answerers and expect them to be followed through on every time. The best you can do is to politely give constructive criticism and if they refuse and their answer is still lacking, then let the community decide whether or not the answer is complete enough without your suggestion.
1. Note that this is a little more lax on meta, as the goal is to promote more back and forth exchanges.