To me it's not so much the health risk (or lack thereof) in using margarine, it's a matter of taste. Butter tastes better to me, and that's what I prefer to use. Additionally, I derive more pleasure from cooking with products that are "natural" than products which are not. That's an entirely aesthetic choice, of course, and your mileage may vary.
I've read varying recipes for clarifying butter, but when I do it it goes something like this: Cut a half pound (or sometimes a pound) of butter into dice, then simmer on medium-low heat long enough to begin seeing a brown detritus on the bottom. I strain the butter through cheesecloth (and I don't try to strain the detritus) into a glass container. I suppose you could store it in the pantry, but I've got room in my fridge.
At any one time my fridge tends to have small bowls of rendered fats that I've saved from various cooking processes; bacon fat, duck fat, chicken fat, etc. Using those fats alone or in combination with others is a nice way to add another element to a dish.