I haven't made a cider in a long time. I'm not sure what you're worried about - if it's contamination, anything living on the fruit will be in the cider as soon as you throw the fruit in, taking the fruit out won't change that.
If you're worried about extracting something nasty from the fruit, that will depend on what kind of fruit it is, how much there is, how you treated it (seeds or skins removed? diced or whole? frozen first?), and the composition of the cider.