I first learned this trick from One Little Bird Designs and it seriously changed the speed with which I can change the color of a layer. Hope you find it helfpul!
A video follows if you find my instructions confusing.
1. Select the layer you want to recolor and click the little square icon (circled on the right). This will make a little lock icon show up on your layer.
2. Using the fill bucket (G) fill the layer.
3. The semi-transparent, aliased pixels are safe!
4. If you're working with colors that are closer together and you only want to change one of them, by lowering the value of tolerance (middle red circle) you'll lower the color values affected by the fill, ie: the lower the number the more similar the color has to be to be filled.