If custom taxonomy makes sense to you as approach to organization of data, but not as interface workflow then you should consider building custom interface for it.
Some frameworks out there can work with native taxonomies, but provide alternate interfaces for them. So you might even find something fitting already done.
The more low key approach I can think of would be to customize permissions to allow use of existing terms, but prohibit creation of new ones by users doing data entry. You can customize permissions for specific taxonomy when you register it or customize from the user role.
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