Why did Barry in Flashpoint (s3e1) release his captive?

Question

Barry was going to accept losing his memories about the original timeline, but he changed his decision when the Kid Flash was injured and then released Thawne. Why wasn't his mom's life more important to him? Especially, after the 2nd season final where he cancelled all the story by saving his mother?

There were 2 other options:

1. To return to the nearest past and save Kid Flash instead of changing the whole timeline back. He could time travel anywhere, right?
2. To become Flash again taking the place of Kid Flash. In this case he would have to leave some notes for himself in case he loses memories on how to use his abilities and let the team remind him what's needed.

So what was the motivation?

Answer 1

Huge Spoilers past this point for any of the readers that haven't seen the Flash yet.

If I remember correctly, Barry travels back in time to stop Thawne from murdering his Mother and framing his father for her death in the finale of S2. This event completely changes the time-stream and creates Flashpoint. An alternate time-line where Barry still has his family intact.

Barry has memories from both time-lines. He remembers every birthday that he spent with his parents, and also every birthday he spent with Joe and Iris. Barry has Thawne captured and is holding him in a cell that he cannot escape from.

Half-way through the season Barry starts losing his speed and his memories from the first time-line. I'm not a writer of the show so I can't say for sure what their thought process was, but I can guess.

Barry starts losing himself.

Thawne inadvertently helps Barry realize that he lost more in the first time-line than he gained in this new one. Barry watches as his brother almost gets killed right in front of him and that really hits Barry hard. He realizes that saving his mom changed everyone, and he realizes how selfish he was being when he did that. He runs back in time to stop himself and succeeds. Barry jumps back into the future and realizes that everything is not as it once was in the first time-line. This is when Barry FINALLY learns some responsibility with time-travel and stops screwing around with it.

NOTE: I haven't seen S3 in a long time. So correct me if I am wrong.

Answer 2

Barry starts to lose memories of his original time line part way through the episode. He confronts Thawn about this and learns that it is a side affect of the new time line Flashpoint, erasing the previous time line. After Wally dies he realizes that staying here is just not sustainable, I mean without Star Labs he can’t really keep Thawn locked up in a random warehouse forever. He understands that his quick decision to save his parents also messed with his friends lives and I’m sure he feels bad about that, I mean (remember it did cost Wally his life). In the end the episode was more about Barry facing his mother’s death than actually saving her.