Use a timer unit to schedule your service start times. A timer unit is flexible enough that you can use a single one to schedule both the initial run, 30 minutes after boot, as well as the repeats 48 hours after the first run. (And you can even decide if you want it 48 hours after it first started or 48 hours after it finished running.)
Description=rkhunter check with zenity findings
Description=timer for rkhunter check
Note that you don't need an
[Install] section in your service unit, since you don't want to "enable" it, as that would run it during the boot sequence and what you want is to only run it 30 minutes later.
You'll want to enable the timer unit, so it actually gets enabled on boot and starts the service unit at the configured times. So:
systemctl enable rkhunter.timer
If you previously had the service enabled, you'll want to disable it explicitly, since it should now only be started by your timer unit:
systemctl disable rkhunter.service
If you never enabled this service before and are implementing this setup from scratch, there's no need for that command.
After you reboot, this should work right as you described your requirements.