That's a bit of an extreme reaction. Always try polishing first, lol. Last year I had a dead worm stick itself to my front wing, and morbid curiosity of how long it would stay on the paintwork outweighed my normal 'get it off pronto' philosophy. It was over winter and the car didn't get washed for weeks and the worm stayed stuck, until I caved and washed it off. Sure enough the paint underneath was etched - not like bird poo etching, but hazed and faded where the secretions from the worm had pervaded the clearcoat, it came off with DA no problem, much like the greasy sun cream stains. Sometimes you have to experiment!
ha ha!
As for the repaint job - I think it was a case of not knowing any better (on his own behalf as well as the bodyshop).
A good few years ago, I had recently gotten a new car and was about to go on holiday. So rather than park my new wheels at the airport, I parked it at my parents house... In mid April... and they have a couple of "Cherry blossom" trees in the garden that were in full bloom... I came home and the roof of the car had loads of petals on it. Every one of them had etched the paint 
Modern water based paints are just so bad at resisting this stuff and I just don't believe (from expensive experience) that coatings/sealants/waxes do anything much to prevent it.
I've seen pics similar to what you describe with the blossom, so pretty and yet so destructive! Modern water based paints are awful and not just automotive - house paint is crap now. My other half owns a painting contracting company and he has seen the changes over the years. Being a big fan of eggshell paint for woodwork, I remember how durable it used to be when it was oil based, since it became water based, even the pricy stuff is just not up to the job, one hard knock and it's off the wood, no matter how well prepped and primed and no matter how many coats.
I'm not doubting mcmaddy's experience, but I have to agree that I do not believe any coatings can stop etching completely. As for sealants and wax, not a chance. The degree of etching can also depend on the diet of the offending bird. Seaside gulls that eat all manner of crap seem to have very toxic sh!t! I live 7 miles from the coast and we get lots of seagulls and if one of them targets the car, and on a sunny day, it etches in minutes!