While Clowney is loaded with talent, he never looked like a great fit on this defense. At least not worth top dollar in the open market.
One of the things Pete mentioned in his end of season press conference is the team needing to be faster on the edges. Clowney, while fast for his size, is not a quick twitch player. He's more or less a blend of strength and speed and while that can work for some teams, the Seahawks have a defined role for their DEs. They played him at his best at the Leo spot, but that meant they had two DE's that are more power than speed, resulting in them getting beat to shit on fly sweep plays.
I am not enjoying the idea of going into the offseason with a huge hole at leo DE by not re-signing Clowney, but I think it's the correct, long-term move.