While I don't agree with this agreement, I don't see any particular problem keeping the negotiations and drafts secret. I mean, the final deal is obviously made public (otherwise there would be no way of enforcing that countries abide by it), but I don't think the negotiators needs to disclose every thought they brainstorm. It would create a lot of public and political pressure on the negotiators and instead of trying to reach something that every country can agree on, they'd be trying to appease domestic lobbyists.
They're already trying to appease domestic lobbyists; making the process public would risk them having to satisfy the public, and since no part of this has any correlation with the public interest...
The problem is that there's no agreement. It's kept secret because they know the people don't want the law. There's no need to keep just laws secret, because they don't offend the citizens in whose name the country is ruled.
ACTA is a corrupt and abusive law. Enacting it was treasonous, especially because the public had already spoken.