Christian,
I've thought about it more too. I think there is a distinct difference between image manipulation and content manipulation.
I'm very much from a slide-shooting background. Once you depress the shutter, you're done...and honestly, I like that. I've pulled whatever tricks I can out of the hat, and used my artistic tool of choice, the camera, to make the picture...but then it's just some chemistry, and voila! That's what I end up with.
I'm treating digital as just a shortcut...not it's own art form. If I had imagined a scene in b&w, on HP5, with a black border, that's where it will end up...I don't care how I get there (and digital will let ME do it, save money and time).
When content starts getting manipulated, it's not a bad thing...it's just not necessarily photography in my eyes. Of course, that doesn't mean it's bad, and it's not a judgment in my eyes, it's just not something you can do in a camera...you've simply used a camera to get the pieces to finish your graphic illustration.
So, that's why I think using SilverEfex Pro 2 is still true to the photograph.
Using a grad filter when exposing is manipulating the scene to make it photograph like your eye sees it, right? Here's a question...how about using a grad filter software package to do the same thing? I think, ethically, you've done the exact same thing. The difference, in my mind, is a photographer does it with his camera and lens, a graphic artist can do it to any scene in the computer.
Arguing ethics in photography is a slippery slope right now. In the beginning of the "digital" revolution (evolution?), only straight-out-of-camera images were accepted. Then, they allowed RAW, which justified levels adjustments (changing what the camera sees). Then, dodging and burning were allowed, just like wet printed photography. Then, we're seeing Hipstamatic iPhone pictures in the NYTimes, presented as news AND art. So go figure. I think changing content is where the line is drawn...but adjusting the image, either by contrast, adding a border, using grain, reducing exposure...is now accepted as photography.
Of course, photography is personal and singular (thank God!), so if a person was to only consider wet plate collodian REAL photography, they can practice their art and look down their nose with pretension at poseurs and there cellulose acetate technology!