It's done this way so that the individual products show up on the order. This way you can keep track of stock and profit margins of the actual items that are sold. This becomes especially important if something breaks during shipping and they return just that one thing.

When prices change, you'll have to at least check your product kits no matter what happens. However, you can put in negative values in the discount field to lower the price by that much. You could put this on one or two products in the kit to it's less of a hassle.