The Skrull factor is a big one, but yeah, due ro public unrest, Tony was trying to accelerate the registration process to avoid more Johnny Storm incidents. While amoral, using the Thunderbolts made sense. Starting a war with Namor would've forced the heroes and government to officially work together. With the state of the country, the government wouldn't trust the heroes without them registering. The Negative Zone was extreme, but we know that neither Reed, or Tony, would keep them there forever. At some point, they wouldn't have to keep them imprisoned to get them to sign.
Honestly, if not for Meik, or the Skrulls, Tony would've made things better in the long run. Not saying that Tony didn't make amoral decisions, but his way paved for a potentially better future than whatever Carol is trying to do.
By the way, does anyone remember why BP got involved?