It's an interesting question. I think I'm with Tracey in prefering the first option, but before tolerance the quality of resistence is important. The ideal garden lilies would be highly virus resistant, but if they did become infected they would also be tolerant: able to remain healthy-looking, garden-worthy and beautiful.
The second choice seems futile to me, as we don't live in a virus-free world, and "very few" could never be none. Susceptable lilies will therefore inevitably succumb. I'd rather live with the whole range of life indefinitely than consider my lilies as disposable.