One of the main reasons why Tess allows Alec to kiss her good-bye is that she has learned that he won't give up until she lets him do what he wants to do. If she just lets him get it over with then she can move on with life and leave him. Hardy uses the word "perfunctorily" to describe her allowing him to kiss her cheeks (47). He realizes that she won't willingly allow him to kiss her lips, though, and that is when he admits to himself that she doesn't truly love him. So, if Alec can realize that she truly doesn't love him, then it is easier for him to let her go on with her life. These two have fallen into a horrible pattern of behavior that wasn't reflective of a healthy relationship, and Tess knew that. She loved him in a way, but she knew that she would always harbor resentment for the fact that he selfishly seduced her and tricked her rather than courting her for marriage in a respectful way. By that point, too, she was done living a lie and needed to get out. A minor kiss on the cheek wouldn't change her mind, but it would help to move Alec along so he would leave.
Enotes.com eText pg. 47.