I remember once (I think my first pixel job) I was doing some work, where a shape was needed to be embossed on a small sprite of a door. I cut the shape out and did a layer effect in photoshop, then reduced the palette thinking it looked great and nobody would ever know I'd been so cunning. Although it never looked absolutely terrible, the tile was rejected and I ended up redoing the shape by hand. I was confused and annoyed at first. It looked better than anything I could do by hand! The shape needed at least a little AA to look like the shape at all at this scale (I think it was a star), on top of the effect itself. But actually, the hand done version was cleaner, more precise, easier to read and more consistent with the other graphics.
By all means, use all the tools available, but if you find yourself saying "better than I could do pixel by pixel", I'd suggest at least see what's different about the result, work out why it's better, and see if you could just apply this directly with pixels before settling for CS4's dark arts. A lof of games (fighting games for instance) use a lot of blend modes and glows atop of normal pixel art in software, and the world hasn't come to an end, so I wouldn't say it's taboo in itself, but shortcuts need a bit of scrutiny to make sure you end up in the right place.