The main arguments really boil down to two, now that the spelling and mathematical issues have been resolved by the latest peer-reviewed experiments:
1) The mantra in anti-codes circles that seems to have made its way to the uninformed general public is that the same effects can be found in any text. But the critical point that is missed is that we measure the effect in the Torah precisely by subjecting thousands of comparison texts to the same methods, as detailed in our protocol descriptions and only the Torah exhibits statistically unexpected behavior.
2) Initial responses to questions about the Torah text's accuracy are reinforced with more recently published points (see "Harold Gans Responds").
Worth a look:
Other critical points appear in the article by Levitt in the same link.
The anti-codes arguments are further put to rest once the reader becomes familiar with the accumulated results presented here.