Answer:
Yes she does love him, it was a slow but sweet relationship that started from when they first met and grew on from when she nursed him back to health. It is confirmed for the viewers when she gives him her mothers ring before the battle of Jachin Due at the end of SEED in which she asks him to return to her solidifying her feelings for him once and for all. This relationship is only more solidified in Destiny with all the shots they have together leaving no doubt in the viewers mind that they love each other deeply.