Ok, but remember what happened is unprecedented. No GM would have protected Song, people who fit his profile don't get picked. Can you think of one guy who has only pitched 17 innings in A ball above rookie ball and hasn't pitched 4 years that has been picked up in a rule 5? It just doesn't happen.
Protecting replacement players doesn't matter here because we are talking about the type of guy who doesn't get picked, wheres a replacement-level player is going to add more value than a kid who could get shelled at the MLB level. Teams don't protect guys like Song.
This doesn't mean pitching isn't a concern, the Sox ability to draft and develop pitching has been lackluster, or it would be disheartening if the Song move worked out for Philly. Those things aren't mutually exclusive from the fact that not protecting Song made sense. Getting upset over Song being picked because of other deficiencies within the Sox system is unreasonable in my opinion and it appears the pundits who all wrote about it agree as well.