I think on Shoma's part it was moreso he was happy that the pregnancy wasn't the product of rape than it was "oh yay I'm pregnant with Kanata's kid!" When you experience a strong psychologically and physically stressin' situation your mind will do some mental gymnastics in order to keep itself intact.
The abortion was part of his hormones changing, Kanata leavin' and him thinking he won't return and Shoma thinkin' he wouldn't be able to provide a good home life for the child since he'd be a single omega father. You can tell he didn't want to go through with it by the time it came down to sign the papers.
It was a lot to cram into one chapter and a lot of the time this happens due to cut budget, editorial staff decisions and deadlines-- which is pretty sad 'cause a lot of the time stories like this would truly benefit from havin' at least 2-3 more chapters of actual plot before they add the cute extra at the end.
This exactly ^
The rape was so contrived. It's like the only reason she's raping is because it's Omegaverse and she's an Alpha but also acts like she was the victim? Not to mention going from "happy to be pregnant" and then suddenly abortion. And that was only in half a chapter what the hell? ┑(￣Д ￣)┍