Maybe this can help - when a drug you are taking reports side effects, it's because someone at some point in one of the phases of the drug trials reported that symptom. Does it particularly mean that the drug caused that symptom? Not really. Someone could have lost some sleep the night before, or been particularly stressed out, or just happened to be unlucky, and gotten a headache and they reported that symptom. It could be totally unrelated to the drug, but "headache" gets put on the side effects list.
Some doctors are unsure whether PPIs actually increase fracture risk. It's really more of a problem with steroids, and even then, it's not that huge of a problem unless the patient is already predisposed to having issues with bone density (women in menopause, etc).
But, there are still alternatives to PPIs if you really want to switch. I honestly recommend continuing some sort of pharmacological treatment. Ginger and licorice are okay. They may work for you, but then again they may not.
There's a reason beyond just your personal comfort as to why you should not just suck it up and deal with GERD. The less controlled your GERD is, the more your lower esophagus gets exposed to stomach acid. The problem with this is that your esophagus is not at all designed to withstand the damaging properties of stomach acid. It's made up of a completely different composition of different cells than the lining of your stomach and will be damaged by the acid.
But it doesn't stop there. Your body is sorta smart and sorta dumb. Repeated exposure to the acid will actually cause your cells to change in an effort to protect themselves. The cellular lining of your esophagus will actually transform and become more like the lining of your stomach. Unfortunately, this isn't perfect. These cells aren't actually meant to change. They're just doing so as a last ditch effort. This condition is called Barrett's Esophagus.
Whenever cells change, it increases the risk of something going wrong in cell division with that change, and completely messing up the properties of the cells. That's cancer. The risk of developing adenocarcinoma of the esophagus if you have a Barret's Esophagus is 40x that of a person with a normal esophagus. This particular cancer is pretty bad, and most people don't survive a year.
So really, you want to protect your esophageal lining. I would personally take an increased risk of bone density loss over an increased risk of cancer, but there are still alternatives. There are histamine blockers. Not benadryl, claritin, etc, which all work on H1 receptors (the allergy stuff). Your stomach has H2 receptors for histamine, which actually triggers more acid release. H2 blockers are things like Ranitidine, Cimetidine, (Zantac, stuff like that), and can be pretty effective at keeping your stomach acid levels down. Antihistamines in general don't have very profound side effects. There are also surgical procedures, but I would try out the H2 blockers first and see if those help.
Also, the problem with regular antacids isn't the extra calcium. It's that your stomach will sense that the pH has raised and the acid content is not as strong. With regular antacids, there's nothing actually inhibiting the proton pumps. Your stomach will respond to the raise in pH by just ramping up acid production, and then you're in no better shape than when you started. It's like adding some ice to your soup because it's too hot... except your soup is still on the stovetop and your stomach just turns up the heat when it notices you put some ice (antacids) in it.
Hope this helps!