Bonner has games where he plays passable defense (the last game vs. the Mavs, for example), but he has a ceiling. He is severely limited physically. He is awkward and slow, can't jump, or move laterally and is a poor rebounder for a post player. All you can ask him to do is give an honest effort and live with the results.
Bonner differs from Jefferson in that, he doesn't produce because he just does not possess the skill to be a good defender. With Jefferson, it's a concentration issue. Jefferson has the physical tools to be a good defender and when his head is in the game, he is.
The main issue with Bonner is, when he is giving a solid effort defensively, it is, usually, at the expense of his offense. Which is really his only value. If Bonner isn't producing on offense, he serves no real purpose. Splitter is obviously the wiser choice defensively.
The responsibility, ultimately, falls on Pop to determine early in the game whether Bonner has his shot and to make the necessary adjustment before it becomes an unrecoverable problem.