I'm of the same line of thinking as you are. It hasn't been mentioned at all since that time, so it's really hard (no pun intended) to say for sure. I mean, look what happened with Olivia, though getting on birth control was never once mentioned in her storyline that I can recall. Just the need to "be careful" (from Graham).
If we recall, they had a direct talk about contraception needs and D not wanting to rely on a condom due to possibilities it could fail, so they agreed on her getting birth control pills after her period ended. They went bareback again at her request, because she asked the MC if he wouldn't mind pulling out as he had before. It's not an ideal method to say the least, but at least her intent wasn't for him to push in his Thunderstick™ to the hilt and blast every sperm he had directly at her egg.
She also noted that spotting and cramping symptoms had recently started, which she said usually happened soon before her period began. At that mention, the MC showed relief that it wasn't a sign of her being pregnant (that they knew of), and she thought to herself that - although she wants kids someday - it made sense to her that the MC wouldn't think now was a good time for her to get pregnant. Again, no devious stuff going on with D.
As they left on their trip to the coast and a new life together, she reminded the MC to stop at the pharmacy for picking up her pill prescription, went in to get them and returned to the car, saying it was easy to do since speaking with her doctor about it.
They both talked about the importance of her taking them about the same time each day, as well. Once more, both in agreement on the desire and need for contraception.
In their first day at Seaside, she confirmed to the MC that she took her pill that morning ... then sexyfuntime commenced in earnest!
D hasn't shown herself to be manipulative like her mother. If she's pregnant at this point it would be due to a complete mistake, IMHO - such as, those symptoms she experienced weren't signs of her period but the start of her pregnancy (i.e., implantation bleeding) and which can occur about a week or so after the egg is fertilized.