So, assuming that safety and code requirements are not an issue, can you think of any reasons to get rid of it?
You say you're covering it with a deck? It's possible that one or more of the posts will need to be cemented into the ground right where the cistern is now.
I guess I would fill it in anyway, just to know that no kids or pets would ever fall in and drown, especially if a section of it caved in and left a small hole in your yard big enough for them to fit through.
A cement cover gives you no gaurantees as cement cracks and breaks quite easily. Not to mention if the ground supporting the cement lid collapses.
On the farm I grew up on, we had a cistern cave in as my brother was driving a tractor over the edge of it. It was pretty deep and had water in it still. We never knew it was there until it caved in. We found another one too, a couple years ago under the kitchen floor when we gutted the same house and pulled up all the floor boards.