Chocolate chips aren't the easiest thing in the world to shoot, particularly if they have been exposed to any temperature shifts (like sitting in a cabinet over the summer). It's perfectly fine to eat when them if they have bloomed, particularly if you are cooking with them. However, a photo will make any blooming look even worse, especially when shot close up. One trick often used in food styling is to brush on a bit of oil. However, that basically means you are tossing out completely good chocolate (oily chocolate... ick)... and in addition, I think it makes the chocolate look unrealistically melty. Instead, I recommend this trick... use a hairdryer on low (ideally with a diffusing attachment) to very lightly melt the surface of the chocolate. It won't get rid of all of the blemishes, but it will do a pretty amazing job of evening out the surface enough that you can then use the clone tool in Photoshop to even out the rest. If you let the chocolate sit for just a minute or two after drying, the surface will become less shiny and look solid again. Be sure not to move anything during this time though, or you'll end up with chocolate smears. Here's a shot from some melting drops I took this morning. The first image is straight out of the bag. The second is about a minute and a half after blow-drying, when the chocolate has firmed up somewhat. The final image is after fixing the small blemishes in Photoshop.
It's important not to let the chocolate sit too long after warming it though or you'll end up with even more serious bloom... here's the same chocolates after sitting as long as it took me to write this post.