What a let down, and to be on your first (or one of your first) hybrid crosses, it's particularly heartbreaking.
It is common for the same virus(es) to show up somewhat differently on different lilies. And of course, who knows what it might do in altering the flower. Very intriguing, indeed. Frankly, I think the virus pattern on the leaves is quite beautiful, but pretty scary and I would be afraid of an epidemic. This virus (or more likely, group of viruses?) seems particularly vengeful. Could you enclose your seedling, pot and all in a tight weave cloth to keep insects out? I am thinking of something like what organza bags are made out of.
The other thing to think about is that if this virus(es) showed symptoms on Pink Giant that is heavily lancifolium (know to be very virus tolerant), it is likely very devastating to other lilies.