const unsigned char * to std::string

You could try:

temp_doc.uuid = std::string(reinterpret_cast<const char*>(
      sqlite3_column_text(this->stmts.read_documents, 0)
  ));

While std::string could have a constructor that takes const unsigned char*, apparently it does not.

Why not, then? You could have a look at this somewhat related question: Why do C++ streams use char instead of unsigned char?