I think that abraded galvanizing and rusting chain is one of those cruising "givens", and every place we've been we've gotten embroiled in the latest iteration of regalvanizing chain. We've tried a bunch of solutions, and found that hot dip galvanizing is the only effective solution. But it is a pain to lug all that chain to some galvanizing plant and waiting a couple days for it to be done, then lug it back to the boat.
I don't think it's worth it to regalvanize only part of the chain, and I think that introducing a weak point in the chain by cutting it and rejoining the chain with a joining link is unnecessary. Most cruisers do what you hesitate to do, which is swap the chain from end to end. I think you're far better off letting the chain corrode evenly over its entire length and then having it regalvanized. When you pull all the chain out to swap it around you could probably treat the rusting section with something like Loctite Rust Treatment that doesn't need to have the rust removed before applying it as a protectant, so you don't have a grotty chain locker. Then, when you finally wear the galvanizing off most of the chain, you can regalvanize it all.
What is the bottom like where you've been anchoring? You should find some nice coral sand to anchor in - I think that your chain would keep its galvanizing a lot longer.