Let me see if I understand you.
You have (already?) commented on Friend #1's post. You do not want Friend #2 to see that. Is this only for one post, or for any posts on Friend's pages, photos, links, etc.?
See, the problem is one of granularity. Facebook has over 1.3 billion users. There are (no lie) trillions of alterations happening to that database every single day. Most settings just are not that precise, because they really cannot be. The Facebook database would not be able to handle that.
Here's what you can do:
1) Want to say something to Friend #1 that you don't want Friend #2 to see? Send Friend #1 a private message. Problem solved, unless Friend #1 copies and pastes the message to Friend #2. There nothing stopping that from happening.
2) Create a Facebook list with Friend #1 on it and any other person who you want to gossip about Friend #2 with. Copy the original post, whatever it is, and share it with the list only. Once again, nothing is stopping anyone from copying and pasting and placing your comments elsewhere.
3) Exercise some self-control and don't talk about Friend #2 behind his or her back anymore, and delete any older comments. If they were already copied and shown or sent to Friend #2, then you're out of luck. Facebook will not go in and delete someone else's private messages or posts for you, unless you can prove that they are spam or porn, and this clearly does not fall under either of those categories.