How to solve protesting about high rent

No - I wouldn't be worried about overwriting buildings. From the beta testing I did I didn't notice any negative effects from destroying properties while placing new structures.

You are right that overlapping a structure over an RCI zone will not dezone that area - meaning that any buildings destroyed will free up the remainder of the space to allow new RCI buildings to be built in the smaller space that is left.

Destroying the RCI building would have removed the home or job for whichever Sims live or work there, but the employment model in SimCity is that agents simply travel around until they find a workplace requiring the type of agent they are (ie: high wealth).

In the event that any unhappiness is generated by the placement of the new structure, this would be counteracted by the happiness generated from placing the new structure.

For example, you will generate happiness in the region by placing schools, parks, police or fire stations in a residential area, placing casinos or other commercial buildings in commercial sectors, or placing large industrial buildings (including power plants) in industrial zones.

"we need money" - solve this one first. This message means there are residential workers which cannot find work. Switch to residential view and look for the buildings with low money bars. Add industrial zones to your city for workers from those buildings to reach.

Another possibility is traffic (even foottraffic). Each worker makes two trips. They start in the residential building that spawns them and travel to the closest place of work (industry, commercial, service or specialization). After work is complete they travel from work to the closest place of residence to drop off the money. Workers do not return to their residence of origin. As buildings fill up, the next workers move to the next building - musical chairs style. If workers don't make it back to residential buildings before the next shift (6 o'clock) - they'll start occupying the void left by that shift. This means that some buildings may not get returning workers - and will not get money. Watch worker return paths and clear up traffic. A clear thru road can get a car from one corner of the map to the other corner in 30 minutes.

"Shopper Unsatisfied" - this means that a residential shopper cannot find a commercial building with a matching wealth level that has goods.

First - goods: switch to commercial view. At 6am and 6pm goods will automatically generate at the commercial buildings. The shoppers will come from their residential buildings and buy those goods. If the all of the commercial buildings run out of goods, then you're left with unsatisfied shoppers. Add more commercial buildings.

Note: If you have sold out of goods at 5:30 PM, but have not sold out of goods at 5:30 AM, you should instead add park capacity to satisfy those daytime shoppers. Most parks are open during the day and closed at night. If you add Commercial instead, you'll wind up with unsold goods at night because there are fewer shoppers at night.

Side note: goods have nothing to do with freight. They are two independent systems.

Second - wealth matching: residential agents have a wealth level. The store they buy goods from must match that wealth level. Click on population at the bottom of your screen and switch to details to see the numbers of each wealth class of shopper. Most likely, you have some $$ residential shoppers, but no $$ commercial districts. Add some parks near some commercial buildings to cause them to upgrade to $$. Then your $$ shoppers will go there.