There are at least two issues here.
Human rights of the Pre-Cogs
The Pre-Crime system depends in a crucial way on the constant participation of the Pre-Cogs, held in a (not necessarily pleasant) state that maximizes their perceptive abilities. While the film does not emphasize directly the issue of their rights, by the end it is clear that they are individuals who value an ordinary life and privacy.
Pre-Crime is not always right
The ending of the film proves that Pre-Crime cannot always predict an outcome correctly. Anderton explains that if Burgess kills him, then the Pre-Crime prediction will be vindicated. If he decides not to kill Anderton, then Pre-Crime will be shown to be faulty. This shows us the inherent flaw of Pre-Crime: when the future is made known to people, they have the power to change it. Indeed, Burgess shoots himself.
Although halo-ing is part of the problem, it is not the main problem. The problem is that Pre-Crime cannot always predict the future with certainty. You can argue that they can take steps to investigate a Pre-Crime report without halo-ing, but any punishment taken may result in a loss of rights for an innocent person.