There's nothing wrong with working the heavy bag. You'll learn a thing or two, even if it "ain't aikido." For example, are you pushing, slapping, or are you really hitting it? When you hit it, does it spin, or did you hit it down the centerline? Is it possible to completely miss the bag, even when it's stationary (yes)? Little details like that...
Granted, it may or may not help your atemi (however you wish to define that), but it sure doesn't hurt to know how to punch a little. Just work the bag, and then decide for yourself whether it's worth spending your time on.