I'm not a biology type so please correct me if I'm wrong.
My understanding of genes and alleles is that when we say this gene controls such, we mean that we found a statistical link between the gene and the effect. We haven't traced the protein and its impacts through every cell and biochemical process.
When we see this allele at the gene causing blue eyes, are we also seeing what else it does? For example, adrenaline increases heart rate, opens airways and increases the emotional aspect of memories.
Is it possible for eye color to be a side effect of mutation/selection for (random example) enzymes in saliva for digesting grain products?
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