It's an interesting thing how they work even though you know what they are doing. That probably explain why people use them as well, they work...
For mothers the case is probably most often that they love their kids very much and for better or worse think they know what is best for them. This is probably also often true for good friends. For other people I would guess it's probably most often motivated by selfishness, but that is obviously both a guess and a generalization so might not be true for your friend.
Knowing what is going on should help you deal with it. Personally I wouldn't try to not feel guilty, it's a pretty useful human emotion, helps you not be a psycho (along with other things). Although there probably are people that should try to ignore those feelings more, or at least learn how to deal with them as it might be a real detriment to someone's life. For me at least trying to understand the motivation behind inflicting the guilt trip and trying to understand why they did it helps. It might also help to try to communicate your feeling about this to the other person, let them know what they are doing as they might not realize how hurtful it is. Although this isn't easy and I'm no therapist so take my advice for what it is - some idiot on the internet spouting an opinion.