Avira,
Did you read what I wrote about ahava? As for Rav Kook, he explained that the people to whom you are referring were did not have a complete knowledge of Torah and could not be put in this category. The Chazon Ish also says this. Even if they were, we would pray for them to do teshuva. This is far preferable and would be a great kiddush Hashem. The Mahaarl also interprets the beracha you mentioned in this manner. Why do you think that it wasShmuel haKatan who composed it?