This topic comes up now and then. For a saltwater tank, it's not natural at all. My tank doesn't even come on until 4 pm (staggered like Marc's tank) and runs until midnight. I work during the day so it's only on when I am.
The other advantage is the lower electricity bill. Most companies have a non-peak hours rate and is usually in the late evening. My total utilities bill is almost never over $200/month, with electric being only $100. I run 2-400 watt Metal Halides plus all the other equipment.
I would try to set up your light to only be on when your at home the most. Don't turn them on and off and then on again.