Japan deserves its fate with birthrates if they continue to write highschoolers like some sort of monks too afraid of sex, making a huge deal out of it.
No, NOBODY with a functioning dick would say no in that situation when the girl you love literally offers the opportunity. Like another commenter said, its just too keep the MC relateable to the target audience. In this day and age, this is just sad and pathetic.
Too many shounen romcoms have two approaches to sex:
1) Character treats sex as if it's radioactive, and the characters stay pure and chaste where they eventually spawn their brood via tree pollination after a time skip
2) Characters are degenerates and compete to sleep with half of Tokyo, and are considered broken or unsavable.
God forbid that sex can be done safely and with respect, and still be enjoyable. I was probably a lot like one of these whimpering manga MCs, and I still was able to get it on during HS. I'll give this manga a small pass though, as the author did warn us that the two main characters were 'pure'.