Yes, biopsies are routinely taken from what appear to be normal areas. I guess you can't always tell; a biopsy is the only way. I know with my first upper endoscopy I had biopsies taken for h. pylori, barret's, and I think, generalized inflammation. Fortunately, I do not have Barret's. I always have inflammation (esophagitis and gastritis), and I had h. pylori. Been through triple therapy twice to eradicate the h.pylori. Didn't appear to be the cause of my problems, though. There are probably other things that they would routinely biopsy for as well--I just don't know what they are. I know that I freaked when my GI doctor told me he sent off some biopsies for analysis. I had the same reaction you did, and he told me it was just routine--good practice. While you're in there, you might as well get some labs out of it because it is a rather invasive test.
Current dx: Rheumatoid Arthritis
Suspected dx: UCTD/Early Lupus
Current Meds: Enbrel, Plaquenil, Aciphex, Ultracet, Zyrtec, Allavert-D, Zantac, Tylenol PM
Past Meds: Relafen, Vioxx, Mobic, Voltaren, Sulfasalazine, Entocort, Prednisone, Humira, Reglan