People, both men and women, hundreds of thousands of them are swallowing semen every day!
I think if there was something harmful about it we certainly would have heard about it before now...
Swallowing semen isn't to everyone's taste and many find just the thought of it revolting. Chance are your girlfriend got carried away and swallowed and now wishes she hadn't...
If you are in good health it is probable your girl's pains are stress related, especially if there are no other symptoms such as vomiting or the runs (stress can cause lots of things including stomach pains), however, even stress related pain should not be trivialised and as with any pain or illness that lasts a week and stays the same or gets worse, medical advice should be sought.
For most people, most of the time, stress related problems tend to subside without treatment after an explanation and reassurance from a medic. Of course the big problem is to be able to tell her doctor what she has done which might be too embarrassing so the practice nurse might be an alternative or the local family planning clinic would be a bit more anonymouse...
To answer your question: I have never heard of that happening before but I have heard of many who give it a try and are heartily sick for a time afterwards...
Semen consists mostly of protein which is manufactered by the body in the body. If the "donor" is healthy and the "recipient" is healthy, The semen should not cause any problems in the digestive tract. If the Problem continues, your GF should see a Dr. because most likely something else is going on. That being said, When she sees the Dr. she needs to be frank about what happened. I can guarantee the Dr. has heard it before and won't be shocked and won't judge her.
Knowing Dr.'s as I do, She or he(the Dr.) wouldn't admit it but she/he's probably done more shocking things if we only knew. She/he'll probably not think twice about it.
I really don't have enough information to make a solid call on that one.
PRESUMING that you are healthy, (i.e. no std's now or in the past, no weird symptoms, not immune compromised etc...), I would guess that it is more likely her difficulty. It could be totally unrelated. she could have picked up a digestive system virus about the same time as the event you describe.
For example, my wife has a rather sensitive digestive system. She gets an upset stomach if she takes tylenol on an empty stomach. It is rather rare for this to happen, although it's not unheard of. Tylenol does not usually cause stomach upset when taken according to package labeling/directions.
It could be just psychological(i.e. fear or just grossed out by what happened and not being able to come to grips with herself having done that).
Only a careful investigation by a trained professional will really tell the tale on this one.
Wish I could tell you something more definitive as an answer, but you'll either have to wait it out and see what happens or have her see a Dr.