Well, that's a little bit unclear. I can understand you thinking that, after all, I'm a "Saeko x Takashi" shipper myself, though one has to take into account the situation they're in: "Them" everywhere, supplies scarce and all buildings containing life are sealed up. I doubt any such contraceptives would be considered valuable at this time; who would have sex during a zombie apocalypse? Yes, there were a couple of perverted individuals, but they were killed off fairly quickly. When we take into consideration Takashi's ability to be collected and rational in tense situations, and Saeko's lifestyle of honour and respect, I think that they would manage to resist their carnal desires. I think Saeko was adjusting her skirt the morning after because it was a little loose, and I'd also like to think that the kiss did happen both versions, though it was only seen in the animé.
In any case, I guess time will tell if they did, or if they will do so later on.