The money spent on Bonner could not have been spent elsewhere. The Spurs were able to sign him using his Bird rights and still use any part of the MLE and/or LLE. If they had not signed him, the exact same exceptions would have been available.
Novak is an inferior shooter, defender, and rebounder when compared to Bonner. The team would certainly be better by exchanging Bonner for a player worse than him in every conceivable way.
Just so you understand. I'm not suggesting that Bonner is great, or versatile, or anything of the kind. Only that complaining about his shortcomings is ridiculous coming from someone who suggests replacing him with a lesser player.