People who don't take Fosamax get jaw problems too. To date, the only
documented cases of Fosamax related jaw necrosis have been cancer patients who've taken it IV. If you did, however, have some problem with jaw necrosis, the bone will heal, just more slowly.
You don't give your T-scores or fracture history, but I'm suspecting you're in the osteoporosis range since your doctor has prescribed a medication. I can tell you that if your fracture risk is high - the benefits of taking an osteo med that has been proven to reduce your fracture risk far far outweigh the risks of taking a med. Once you've had a vertebral fracture, there is no second chance.
With your history of GERD and gastritis, an oral med may not be the best choice for you. Talk to your doctor about Reclast, the annual IV med or IV Boniva.
You say you can't take Vit D or calcium. I don't understand what prohibits you from doing that because calcium in the form of Tums is often taken for reflux or indigestion. Vit D comes naturally from the sun (but not enough) and the supplements have not been shown to have an effect on the digestive system.
You should know that any medication you take will not work unless you give it something to work with in the form of calcium and Vit D. If you can't take the supplements, get it in your diet. Read food labels carefully as many foods now have calcium added. You need 1200 mg a day. Your body will absorb about 500 mg at a time.