I think the major moral objection people have to charter cities is that they feel exploitative of the host nation. Proposals seem to take the form "we'll take some rich Westerners, and put them in a host nation where they don't have to follow the local rules, and the host nation will benefit because the Westerners will hire them for labor" - it's very hard to distinguish this from colonialism. Few people think it's a bad thing to have e.g. Indian tribal governments, which are indistinguishable from what a charter city would be.