You can still have sex even when you are not trying to conceive you know! Even pregnant women can still have sex if they want to! you haven't been cheated out of anything, if you are happy about the baby, then count yourself lucky it has been an easy ride to getting pregnant not a long and hard one.
I'm glad you have managed to sort everything out. Remember the time indicator ones are not an accurate science, and the doctors will only be interested in when her last period was really. But if you do a conception indicator thingy, it will probably say 3+, which equals five weeks pregnant. (that means the baby was conceived about three weeks ago, possibly resulting from sex between 3 and 4 weeks ago) of course, she could be further along than that, but these tests don't go past 3+. The scan will tell you in good time.
As for the doctors. There is no real need to see a GP. Generally, what happens is the woman goes to the doctors, and asks the receptionist to make a booking in appointment with the midwife. This is usually done at around 8 weeks or so since the last period. But there is no harm in seeing the GP if she, or you for that matter, have any questions.
And since all's well that ends well, don't be too cross with her. She might have been rather devious but it is frightening for a woman to be confronted with an unplanned pregnancy, no matter how good your relationship is. I guess she was worried you would not have wanted to continue with the pregnancy, especially if you hadn't talked about kids before. She should have been honest definitely, but I think you should probably let this one pass.
good luck to you both with the pregnancy, I hope it goes smoothly.