There certainly are better ways to deal with issues like these. Just as there has been a great deal of help mothballing house, this should be no different. The goal should be to keep business, not run them into the ground, and be the final blow.
If the city can't identify the specific issues that need to be resolved, other than 'entire structure' they are not doing their job. This is stupid. There should be a specific list, along with priority, and along with what would be necessary to keep the business running or open as repairs are being made.
Years ago I was building a large greenhouse, and had all of the wind load, and structural information. No one in the building department could ever tell me specifically (like a check list) what additional was necessary to get the permit issued. Back and forth between departments, you need this, now you don''t go here, go there, etc. I finally paid a general contractor friend of mine over $250 to get it worked out.
This situation is too much like the earlier issues with many other properties in Springfield that were condemned for a leaky roof, or other minor issues.
Really sad.