I think a screen with a more accurate description of the economic status would definitely be helpful. I'd also be OK with a partial cost each turn that the structure is being built, but like you said, it might be a little more complicated than necessary.
As far as going into the negative, though, I feel like that's dangerous territory. If you have a negative income, which can easily happen if you build too many units early on, then you don't have a good opportunity to correct your finances. This gameplay element separates your action/decision from the effects of that action/decision, and gives a very delayed feedback. Consequently, it's hard to correct for either over or under-building. I also have a hard time knowing exactly how quickly I can build without my bank account being stuck in the red.
After thinking about this in more detail, I think I really value the ability to understand whether I made a good decision to build something or if I have overextended myself. With a delayed payment cost, I don't get that feedback.
Civilization helped prevent this by tying the upkeep cost of units to the resource required to produce them (i.e. production units/shields). Building too many buildings too quickly could still put you in negative income, but your ability to expand was more limited early on in Civilization. In Elemental, on the other hand, you can build 3 towns in the first 5 turns, and place buildings in all of them, without any restriction on overexpanding. I'd just like a better feedback mechanism for my money.