I feel your frustration. I had a Nissen in 2009, and thankfully it has worked well. Still, I have a very reactive stomach and antibiotics really put it into a tailspin. Amoxicillin is the one I can take best. I thought I could handle a Z-pac, but found out after taking it recently that it also causes problems. My stomach hasn't felt right since then.
Before my surgery, though, the gastritis would send tremendous amounts of acid into my esophagus, and I could eat almost nothing for weeks. I'd lose 20 pounds, and be in misery for up to 3 months. Once after Augmentin, I ended up in the hospital with uncontrolled gastritis, esophagitis, and (mainly) asthma. The GI docs couldn't do anything for me. They switched me to Protonix from Nexium, but that was about it. It's just a matter of babying it and being patient.
Once I called my GI office asking if they knew of an antibiotic that might be easier on the stomach than others (perhaps he'd had other patients with a similar issue and had discovered something that was not as harsh.). The GI doc actually called me back, and treated me like #$%@$--as if it was an extremely stupid question and dismissed me summarily. That did it...I was done with him! I asked my PCP to refer me to a GI doc I could communicate with, which he did.
I think it's a hopeless cause. Thankfully, my gastritis is contained now, and doesn't migrate into my esophagus, which was much, much worse.
I wish there was an answer, but unfortunately the only one is to avoid antibiotics like the plague!
Good luck with your quest.