This month's Zymurgy magazine has a good article about Short's Brewing Co. use of citrus fruit. They do both depending on the flavor profile. If they add fruit during primary it is usually in the form of juice or puree. If they add fruit in the secondary it is usually in the form of zest or peels.
They say that adding citrus to the primary captures the crisp tart flavor. Adding zest in secondary is similar to dry hoping giving it more an aroma.
They use all products that are delivered to them sterilized. They did say if you use fresh fruit to soak them in no rinse sanitizer.
There was also an article about using Kumquats. Both recipes for using Kumquats added them in the secondary.
For my wit bier I make I add dried bitter orange peel that I peeled myself. I usually add a portion at 5 minutes and then add the final amount in the primary. I sterilize the portion that I put in primary by removing a cup of wort at flame out and steep the orange peel in this. By the time the wort is chilled the peel is sterilized and ready to go in primary.
I have also made a Braggot with dried cranberries and a fruit beer with red cactus fruit. With both of these beers I bring enough water that will cover the fruit to a boil and then add the fruit and cover and let steep for 20 minutes. I then put the fruit and water in a sterilized blender and make a puree that I add to the primary. For the cranberry puree, I used a bag since there were a lot of skins. For the cactus fruit, I just poured it in. There were seeds but they settled to the bottom with the trub.