She definitely still understand him 100%. Just when she came to know he had arranged a party for her and she could not make it. She immediately understood what Samrat must be going through. She could not do shoot because she was anxious for him. She searched for him in all college. She made a time table so that they can spend time together. She is doing all this when she already have more than enough on her plate with shooting. She is still taking care of Samrat. She became bad in his eyes by asking him to say sorry just because he does not go to jail and other people related to film do not get affected. She still cares for him the most and she still can understand his inner feelings.
About being hurt by Samrat's outburst, there is nothing wrong in that. Both of them have never hidden from each other if they are hurt. Gunjan told the same to Samrat after she came to know about bet how hurt she was more than once. They both were hurt by each others' behavior after Suhani truth came out and both of them talked to each other about that even after their reunion. Only because they do not hide such things from each other.
I am very happy for Gunjan not leaving the film (I want the film to get axed though) because if she left the film, she is leaving her job in between. Gunjan we all know never turn back once she has made commitment. She completes her job always. She is being Gunjan by decidng to complete the film and I respect Gunjan for that.
Please do not blame Gunjan for Security Guard's arrogance or for Samrat's insecurities. She is doing all she can to help Samrat. She cannot leave her shot in between just to go and make sure Samrat is okay. That is not possible and practical. And she has full right to be hurt when Samrat thinks Neel and his film is coming in between them when she loved Samrat beyond anything else.
I am not saying this is Samrat's fault either. He has his own reasons to be insecure and possessive. I can totally relate to him.
Just as Gunjan says in her dialog of the film today, "Ye na tumhari galati hai, na meri. Ye waqt ki galti hai. Waqt hi hume paas leke aata hai aur waqt hi hume door leke jata hai".
Please spare a thought for Gunjan's suffering and dilemma too when we are worrying about Samrat just because he is feeling left alone.