You realize that as presently stated that's the only way for the Wraith threat to end, either genetic manipulation into something that's "nicer" to us or extinction, since humans can't coexist with them, not unless they have another food source.

It's always self defense for humans in Atlantis, since it's been established that a Wraith can't not feed, he / she might not want to, but if the going gets rough enough, that's what's gonna happen, and at present we're it, we're their food source.

These are SGA's options :

a) Die fighting an hopeless war.
b) Run away like the Ancients did, and allow millions of humans to die.
c) Kill the Wraith down to the last one, since we can't coexist.
d) Change them or all humans so we can coexist.

Exactly were are SGA's ethical choices?

Oh, and of course, from a S1 episode, there's always another option, one that someone has already thought of before.

e) Remove the food source. Kill (since transporting them isn't viable) all humans in the Pegasus Galaxy.

Or, taking SG1 into account...

f) Show the Ori that there's another Galaxy filled with humans.

Without some changes to canon, to the Wraith as we know them, there are no ethical choices.