I don't see how it's possible to get around some of that. Look at the descriptive text for just about any evil monster ... unless you change all of that what difference does it make? I do agree that it should be reinforced that the entries (including alignment) are just a default.
When it comes to PCs I think TIBF can just as easily abused. The guy that blamed asinine behavior on alignment is just going to blame it on an ideal or flaw. That's a player issue, not a system issue.
It's a community issue not a player or system issue.
The problem with alignment really isn't monster monsters. It's humaniod monsters.
There's nothing wrong with always Lawful Stupid Paladins, CE orcs, and LE githzerai per se, as long as one recognizes that it is weak storytelling used for filling if the DM isn't going in depth in it.
However large swath of the community would object to being told that their settings have weakpoints. Especially if those parts are directly lifted from a MM. But weak lore is weak lore.