You could code up something in the deploy hook to select the master node (mostly the first instance in the layer) to run migrations and you could disable the "Run Migrations" when you deploy. I do this for the Rails app in my company.

I actually solved this with our custom deploy script. We choose the machine that runs the migrations.

The necessity of building and maintaining a custom deploy script is the biggest wart for us (though I admit that the API is pretty good, and said script has not had that much maintenance overhead).