It was high time he took a stand and revealed his discomfort. I liked that he talked to her sternly, nothing bad either, didn't bring other people in between and asked for space... for her own good. Siddharth might be many things... but he did the right thing here. Maybe he did it after he saw how Sana was mauling Gulati and Kartik (that it was a regular issue with her)... or maybe he did it because he thought Salman was giving him a hint, saying who knows kaunsi baat audience ko na pasand aayi ho... or maybe Sana was chipkoing to him under the blanket and he was actually, really done (coz Sana did mention pehle achha lagta tha something) or maybe he sees no other option now and wants her to get used to the detachment (he did mention his friends outside the house are not like her).
Whatever might be the reason... they need to close it and move on with their respective games.