howdy,
I am sure you will get a lot of links to all the info that is out there from people if you haven't already checked out the topic.
As to your specific question, while there is some evidence that points to non-religious reasons why one might refuse a blood transfusion, all of these reasons, benefits and percentages are far outweighed by the benefits and medical effect of receiving a transfusion.
Secondly, the position (interpretation) that Jehovah's Witnesses have on blood has been sliding towards gradual acceptance of Blood and the ultimate discarding of the current ban on blood (doctrine). A few feel, and I am one of these, that it is a certainty that Jehovah's Witnesses will ultimately accept blood transfusions and discard the old doctrine. Exactly when this may occur, if at all, is a matter of debate, but I believe that it will happen over the next 15-20 years.
Obviously, it sounds though that what you are dealing with is your girlfriend's personal convictions, and since she isn't an active Witness, it is hard to say whether whatever changes occur or have occurred within the Org would effect her own views.
I would say that if the differences in worldview, your being an atheist and her being a believer to some extent, are not insurmountable in your relationship then you should not make the blood issue the major obstacle to your marrying her since it is likely to turn out to be inconsequential 1) once she actually has a child and has to face such a situation of choosing blood or possibly losing the child 2) that you may be able to reason with her and convince her over time or 3) that the Organizational changes may influence her view.
If it is at all possible, and if she really really desires to marry you, perhaps she would be willing to sign a written agreement that sets forth that in an emergency or the development of a life threatening illness that blood transfusions and blood products will remain a medical option and if you choose upon the advice of a doctor to allow such that she will not attempt to prevent it. Have an attorney draw it up (get a prenup while you are at it) specify the child(ren) and get it signed dated and notarized and redo it every 3 years and every time you have an addition to your family.
-Eduardo