Personally I would take a doctor's advice over that of Internet people.
Even the doctor was basically "I don't know if acid is really the issue or not... we can try Zantac just to take a stab at it" :X
This is really tough. Obviously you don't want you kid in pain if he/she actually has GERD. On the other hand, you really don't want to give your baby any unnecessary meds, especially one than can cause long term problems, like, for instance, as the NPR article posits, necessitating continued use of the drug.
I read a bit of the link you posted and it says zantac can make a baby sleepy!? That's nuts, I can see how babies that don't even have GERD would continue to use it and then subsequently need it.
Most babies, as the link you posted states, have "reflux" to some extent. It's why most babies spit up. As a nursing mom, I had oversupply, overactive letdown, and I thought nursing was the solution to ALL of my baby's problems. Combine that with an over-eater, and DD1 was a spectacular vomiter. I called my LLL leader a couple times late at night because of the amount and projectile nature of her "spit up." But I never ended up with a GERD diagnosis, probably because even though I'm sure I told the doctor what we were seeing, I never said, hey,doc, could it be GERD? (But our ped is not really rX happy, fortunately for us...) I am very careful to only describe symptoms as they are to my doctor, I rarely suggest a diagnosis, since I'm an accountant, not a CPA. Because I sometimes think doctors are just quick to agree and give you a prescription and get you out. I once had a doc write my an rx for antibiotics for poison ivy. I didn't fill that.
If it is regular old reflux like my baby had, you can try some things to help it out. When I let down, I'd actually pull baby off for a bit and just soak up the milk with a receiving blanket until it stopped- so DD didn't have to voraciously gulp everything that was shooting into her mouth. (Sorry if this description is weirding anyone out...) I think she'd consume a little less that way, and she'd have to work more for the hindmilk, which is the good fatty stuff. If supply isn't a problem but you think too much foremilk could be a problem, try block nursing- one side only per session, save the other side for another session. This method of one side per session is often suggested to help moms with oversupply get it in check, so be careful. But it also means more hindmilk if baby will continue to work for it on that one side.
After nursing I'd keep her upright if at all possible. Lots of babywearing (read up and practice safely!). My LLL leader also suggested when we do lay her down, elevate the top half of her body a bit. You can do this safely by putting a bolster of some sort under one side of the mattress.
Also, maybe pick up the book "the happiest baby on the block," which gives some really great practical tips on how to calm a fussy baby from about 0-3 months. It was a lifesaver for us, once we were comfortable with the fact that there was nothing wrong with our baby except that she was acting like one.
Try to pay attention to the times that the baby is fussy. I have talked to moms who considered a GERD diagnosis, but after they realized that it was always between 6-10 pm that the baby was fussy, they reasoned that it wasn't GERD, GERD would probably be an issue all the time, not at the normal baby "witching hours."
Last thought, allergies are rampant. I also know a lot of moms that went on an elimination diet and determined that their baby had some specific food intolerances. This is a lot of work, I think, so maybe see if some of the other techniques here will help.
kellymom.com is a great resource for nursing moms, if nobody here has mentioned it yet, too.
Okay, I think that's all I've got.