You need to annex the city as soon as it's captured. Because the courthouse immediately appears, you'll get the same unhappiness as you would if you puppeted it. It'll still have the normal resistance and the costs of SPs will go up accordingly.
I personally don't understand why they just don't let iron curtain put a courthouse in puppeted cities too. It's free, so no gold maintenance, and it wouldn't do anything except for sit there because there would be no unhappiness from occupied citizens (because it's a puppet).
So basically, you have to unlearn the newb trap of hitting the annex button as soon as you capture a city. With iron curtain, you really only have two options -- raze (in which case you get a courthouse anyways) or annex. The only reason to puppet with iron curtain is to keep the costs of SPs down; however, that's probably not that big of a concern because you have a level three ideology tenet.
Oh, and also, the annex/puppet/raze screen is messed up with iron curtain. The tooltip for annex will state the unhappiness without a courthouse -- which you will get immediately upon annexing. The tooltip from puppeting a captured city is the correct amount of unhappiness you will get from annexing with iron curtain.
So yeah, just annex or raze everything you come across with iron curtain. The only situation I could see puppeting something would be that you will get an extremely important SP that you absolutely must have next turn. But even if you do annex immediately, you'll probably just wait one extra turn (if that) anyways.