I have watched that scene so many times ...and then realized where the problem was...the truth could have been put a lil differently by Shefali...but then at that point in time , she was in a very horrible state of mind...
Ideally what she should have said is "Naina , you should stand by Sameer no matter what because I am sure he will also stand by you. Don't let go his hand the way your brother has done because it hurts very badly and even you will not be able to live a free life with such a guilt in the mind."
But what she did was to tell her to move away from Sameer in case she cant stand by him...both have the same meaning , its the way its spoken and conveyed that changed the whole situation. When she spoke to Naina, for her Naian is Arjun's brother so she saw them as a TEAM...where as Sameer always took Shefali's help when he wanted to meet Naina or pass some message to Naina...So for Shefali...Sameer in her team ...and hence thought Naina wouldn't stand by her love ...where as Sameer would...therefor her advice to Naina only could scare her ...not encourage Naina to have a successful love life...