while on my surgery rotation last december, the chief of surgery tells a story about a women involved in a car accident. she had a lot of abdominal pain, even though the accident didn't occur at high impact. he then shows us the x ray of the abdomen, which shows a nice healthy fetus in the womb.
moral of the story: ask any woman of reproductive age if she's pregnant, or if there's a possibility she's pregnant. if she says no, you still get the pregnancy test.
most ob/gyn's will tell you that any woman that comes in is pregnant until proven otherwise.
what the doctor in your girlfriend's case is what any doctor would and should do. as someone pointed out earlier, no doctor wants to be the one who orders an x ray or ct scan or other imaging modality only to see a fetus. no doctor wants to be the one to prescribe a drug treatment regimen, only to find out a fetus was harmed.
it's pretty much standard procedure. tell your girlfriend, "welcome to adulthood."