Palin voters didn't get their second choice preferences counted. If they had instead tactically/ insincerely ranked Begich first, he would have won by a 5% majority against Peltola. They were punished by voting sincerely for Palin.
Palin was a spoiler. People who voted for her threw away their vote, period.
If you want to argue that there should have only been one republican on the ballot to prevent a 'spoiler' you'd have to take that up with the republican party
But they forgot one crucial thing: people. Even within the party, there are members and candidates others can't stand. And if you're going to give people choices, you have to be prepared for them to make choices you don't agree with.