Throwing sentiments out of the window, we both know Rakitic hasn't been his usual self for some months now, and he is currently struggling to start games for Barcelona, for me that's enough reason not to play him, it could even serve as extra motivation for him to improve.
That makes sense when you are France and replace Varane with Umtiti or something like that. When you are Croatia, the choice is between Rakitić and Badelj. So, if you ask me, Rakitić can come drunk wearing a blindfold and have his feet stuck in concrete shoes and he'd still be my preferred choice. Same goes for some other positions in our team, including Lovren for example - a player I do not value at all. He will play if he does not get a game for Liverpool for an entire season and it will still be the best thing for Croatia.
Croatia is a good team with some great players. However, that team does not have depth like many other top teams do.