you can do this with the zmprov command
In order to figure this out, I set the preferences from the GUI on my account, then from the commandline did:
zmprov ma firstname.lastname@example.org zimbraPrefOutOfOfficeReply 'whatever you want your message to be' zimbraPrefOutOfOfficeReplyEnabled 'TRUE'
Then I just looked for the values that changed. You can then set any of them with the ModifyAccount (ma) command of zmprov, after you know what the correct settings look like, by doing 'zmprov ma account@domain attribute 'value' attribute 'value' etc. as shown above.
zmprov ga email@example.com