Because Kaname is the most perceptive of them. Ever since that line Gary Stu said to Chisaki (I like the current you or something to that effect), Chisaki has been more conscious of him romantically, blushing at one time when they made physical contact. Now she panics when she sees Tsumugu fall, but didn't when all her close friends started diving in the rumbling ocean. This is understandable because Tsumugu is human, but her panic still felt it went a little beyond friendly concern, especially due to the short time they have known each other.
Also, it wasn't a lap pillow. Chisaki was embracing Tsumugu to her chest and pressing her face against his head dearly. It felt like something a lover or at least a close family member would do in that situation. Kaname's surprise and pain from that scene is perfectly understandable.