Server/proxy coule check database structure on it's startup, log warnings and stop it a critical problem is found.
Partucularly it could check:

• If fields have correct case-sensetive collate (utf8_collate for MySQL) - this happens after upgrade from 1.8 or 2.0 (ZBX-1349)
• Check if table indices are correct
• Etc...

A new command line key should be introduced to skip this check - this would allow peple to run zabbix if they have some custom database configuration.