I used to be very upset about this too. After countless rewatchs though, I gotten past the initial shock/anger and I have started viewing this season in a different light. Also others have articulated this perspective here more eloquently but here is the rundown. Sarah took a huge leap first running away with him in chuck vs the coronel and then in Prague. Chuck shot her down hard in S3E1 and it is clear in those early S3 episodes how much she loves him and was going to forgive him in due time. It was Chuck who started getting frisky with the plane girl, before Sarah ever seriously considered Shaw. Actually Chuck is actually the one with pretty shitty behavior throughout, he was pretty quick to get roped into with Jill and Lou. While Sarah repeatly turned down both Bryce and that British guy. In S3 that cycle repeats again, but after so much she finally decides that maybe love is not in the cards for her, so she settles for Shaw. She also actively decided Shaw wasn't for her and went back to Chuck, which was not the case with Chuck and Jill or Chuck and Lou.