You kind of described why I think it's something of a wonky system. Moral is a control on your population in addition to farms in addition to planet number in addition to colonization techs. You have several systems all basically trying to do the same thing of limiting how many people you can have.
I don't think the systems are there to "Try to limit how many people you have". Its like in the real world. Demographics are affected by a multitude of parameters. You say it in a way that tries to make it sound like it is a bad concept but I do not think so.
It's a tad worse when you consider that population count only mattered in taxes and in invasions.
It also matters for trade routes and influence.
Also moral had that gangly bit where you could easy over build farms and by the time you knew you did, you would have no space to counter act the moral plummet. Lots of stuff you could complain about with moral in GC2.
You kind of described why I think it's something of a Fun system. 
If you build stuff randomly without knowing what you are doing you will naturally end up with a badly functioning empire. Part of my fun in GalCiv2 is have my empire work optimally. For this you need just the right amount of everything. Over do something and it will end up unbalanced.
I do like the idea of moral being like the defense to influence though. Only problem with that is that influence also works as a defense to influence.
Once again I do not see why this is a "problem". You seem to think that a parameter being affected by several parameters is a design flaw.
In conclusion, I am not whining about what I see in the GalCiv3 screenshots. I have fate that StarDock can make a great game even if it is different than the predecessor. I am simply responding to those who say " Good riddance" to the planetary approval system because I am one of those who liked it.