Removing VAs will get rid of the mindset that being a villain is a 'higher-form of rp'--that by being a villain you provide a higher quality of roleplay over Lawful-Good characters. I honestly prefer the "I wanna be the hero!" archetype over the "You don't understand my deep emotional angst" that many villains adopt.
Besides getting rid of the taboo, many non-villainous characters write (improperly named) villain applications so that they're not tethered by the server's arbitrary ruleset for what your character can and can not do.
The removal of VAs may result in an initial increase of villains, but over time you will see that people get tired of banditry or constant asshattery. The taboo of villainous deeds is why so many strive to indulge in it--but they will quickly realize it's just as fun as 'good' rp.
VAs also discourage "letting-go" of your characters, as few people desire to write yet another application that may or may not be accepted depending on the mood of the person reviewing it.
On a personal level, I find "alignments" asinine ways of pigeon-holing characters into set ways of acting, villain applications only exacerbate this.