To be honest, I agree. Sure, I get Yamato being worried about her health, but... this is her decision, and, for her, track and field is still very important to her. She can't be having his kids just yet.
Also, what happened to that condom, anyway? Hattori gave it to him, and apparently it vanished... did he legitimately throw it away? Did something else happen to it? Did it just get forgotten in the intervening year or so, just so the author could throw this pregnancy curve-ball at the readers?
Regardless, they should take proper precautions in the future.
If this story was more recent, I'm not entirely sure if abortion would even be on the table... does Japan have some sort of laws on the books against it with their declining birthrates, nowadays? Just something that's come to mind of late...
...
Oh... another possibility is if the choice is taken away from them- she ends up having a miscarriage. One of the Manhwa I have read in the past year had the female lead lose a pregnancy due to miscarriage, though not all readers seemed to have realized that was what happened, and got real pissy because they thought she got an abortion, all because she was contemplating it in prior chapters, and decided that made her a horrible human being.