considering that puppets are pretty much free ic that can be used by the puppet master 100% by simply trading away the puppets money and supplies for resources that you will get back through the puppet resource limits makes puppets a complete no brainer for anyone and the short term dissent can be very quickly removed by utilizing the puppets money and supplies......Surely creating a puppet is the better choice to maximize ic of the alliance as whole. But it is more like 2 month or more till icd break even is reached. Without the advantages against short manpower(India for extreme) and short resources(Malaysia for extreme) i would still choose for not liberating as i might utilize the ic in a better way. It is manpower and scare resources that make puppets valueable. Still ic would need to be high enough to utilize the puppets manpower.
and your math is correct but you do not consider any long term benefits or advantages, just like you dont consider the cost of infrastructure (and is still very much against sliming down the infrabuilds to make the game viable for the ai)