I don't think it's possible. iTunes requires a full OS install, so you'll have to just run it on a VM. And Apple has things locked down so much that the only way to do full iPhone/iPad backups is through iTunes.
iTunes requires usb drivers to sync with an iPhone. Wine does not support windows usb drivers so even if you get iTunes to work in wine, connecting to the iPhone with it won’t work. You might be able to use libimobiledevice to do a backup.