First, realize that it's not going to be that simple. Minecraft imposes a lot of fake contrast onto the blocks in addition to "real" lighting, so it'll be difficult to key everything out due to that variation. At the very least you'll need to change all of the block models to remove ambient occlusion and shading. You can also use Optifine to make a full-bright lightmap to remove that pesky lighting issue.
Second, there are some things that have hard-coded colors to them like the sky. So if you're against the sky you'll need to key that out separately. Again, you can somewhat solve this using Optifine's Custom Skies feature by making the entire sky a single shade of green regardless of day or night. You'll also need to 'blank' the clouds texture for this reason.
Third, there are a few instances where the game adds colors to things that aren't affected by the textures. Things like grass and leaves where you'll have to edit the block models (again) to remove the tinting. However there are some instances, like water and the colors of potions, where these values are hard-coded and so can't be removed with a resource pack alone. In some cases not even Optifine can help with these. So it won't be perfect no matter what you do.
Finally, as far as just replacing the textures goes, just learn to use batch editing in whatever software you use. I don't know what graphics package you have, but most have at least some form of this. You can probably find decent instructions with a simple search.
Greatly appreciate your reply! I only really wanted to do it for a handful of blocks solely and was wondering if the process could be automated a little easier - I don't think any complex textures or fluids will come into play as I just wanted to isolate my character in post. Thank you for the info!