Assuming 3.5:
>Zone of Truth
Some persons may succeed the saving throw when they first enter, since rolling a 20 on saving throws is an automatic success. These people can lie with impunity. All persons within the affected area are aware they are under the enchantment, and can not lie deliberately - but if they don't know something is or isn't true, this doesn't count as a lie.
Which means this "utopia" is already showing cracks.
>Mark of Justice
It can only be cast on willing or restrained persons, which means you either have to convince them it's "for their own good/the law" or you've got to force it on them, which seems counter to the idea in the first place.
Also, you have to specify a "criminal act" that triggers the Mark. Is it theft? Murder? Sodomy? Fighting on Sunday? Not attending church? Lighting fires on the new moon?
>Detect Alignment
Four different spells. Not including the Marks of Justice to cover littering and jaywalking. There would need to be an entire bureaucracy in place to process even a single person.
Not to mention there's no way to detect True Neutral persons, they simply have an absence of Chaos, Law, Good and Evil. I can see a situation arising where persons of Neutral alignments are considered the least trustworthy.
A simple spell (Undetectable Alignment) would allow a person to smuggle (unknowingly) objects that are Evil or possessed by Evil outsiders into the city. A second spell will prevent Detect Magic from detecting that an abjuration has been cast on the object or creature (Nystul's Magic Aura).
>Forced suppression of magic and supernatural abilities limited to Chaotic and Evil persons
Because no one would employ spies or agents who are Lawful and Neutral, right?
>Protection from Alignment
Won't stop espionage or sabotage attempts.
Honestly this whole city seems like some kind of well meaning nightmare where people have no rights except to obey the ruling classes chosen morality.