I think the options you outlined are basically all we can do, yeah. The second (omit "use asm") seems better to me, although it might be an option in the polyfill or different polyfills might do different things. Overall I don't think this removes an incentive to use wasm (shipping as wasm allows running as wasm natively, which is strictly better, except for the time to polyfill if it isn't), but maybe I'm not seeing something?
But in general, polyfilling has not been a strong constraint on the design of wasm. This means that wasm is less limited by legacy, but it also means that polyfilling will not be perfect. Aside from resizing memory, there are issues with numeric corner cases (trapping vs not), statements=expressions code sometimes being inefficient to translate to JS, and others. Polyfilling will still work, but it will require some caution I think.