Probably one of the longest running debates is to secondary or not. Using a secondary helps to clarify your beer, especially if your a rookie and haven't honed your racking skills yet. Leaving in the primary will clear the beer just the same, but the racking is the key. What you are doing is 'dry hopping' your beer. That's why the directions told you to rack to another vessel and add the hops. Normally you don't want to leave your beer dryhopping for more than a week. I assume you did a hydrometer test to make sure your beer was done fermenting before you racked it to the secondary. Anyway, you haven't harmed your beer at all. I often use a secondary (to make room in my primaries for more brew, to clarify because I suck racking, or to dry hop), and I've never had a bad batch because of it.