It's quite simple.
Just compile in pre-renewal mode to ensure you've got pre-renewal mechanics, and disable any job npc you're not interested to have in your server on the npc/scripts_jobs.conf file.
Then, if you have a job changer NPC, ensure it won't change your players to any trascendent class. Trascendent and third jobs will still be available on the server, just via atcommands or if a script changes them to these classes (this happens on every current emulator), so you have to avoid the usage of these atcommands. No other script than a jobchanger or these specified in the file I linked should arbitrarily be able to change jobs, based on current Hercules version.
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