It's not about the (financial) consequence, it is about the mechanic that doesn't make sense. Players who care about losing countries mostly don't do so because they lost money, they do so because they don't want to lose the country, worked on killing every alien that attempted to turn the country and still lost it because of game magic. There shouldn't be scripted game magic, there should be a self-consistent story.
As for being pushed to go to Cydonia, that's what increasingly numerous and difficult missions is for: Once you are ready, you have the choice to go and most likely win, or stay here for little real advantage but risk getting your soldiers killed in combat.
And really, if someone wants to farm UFOs for fun, I'm not going to argue against that. It is a single player game and we all have various conceptions of what's fun.