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Unless you modify everyone ever, this is extremely unlikely to happen.

There are people resistant to malaria that do not carry the deleterious red blood cell mutation, but a different variant.

Why is that unlikely? As cost approaches zero and benefits increase we can assume we get pretty close to 100%. In fact holding a portion of the population back, even if well meaning, will be discriminatory.

I give us decent odds we end up like the bananas.

1) It's not perfect immunity but rather resistance, and it's when they are heterozygous.

2) Heterozygous still carry the gene and can pass it on (you're likely to just exclude homozygous people)

3) Sickle-cell disease has a lot of downsides... Yes, it's a disease.

There is little to zero downside in preventing births of homozygous affected people.

You simulate and test in lab for an even better mutation. Guided evolution is much faster than genetic evolution.