The fact that the monitor's profile gets embedded is the only way the OS can preserve the appearance of colors in your photos. If you open a photo in Photoshop, take a screen capture (let's say for now via the built-in OS tool), then open this screen shot in Photoshop (and preserve the profile in the file) and compare both side to side, then you will see that the colors are visually similar even though the numbers for each pixel is different from one to the other.
This is all normal behavior. The colors you see on your screen on a calibrated and profiled monitor is actually raw values sent by the OS to the graphics card which then "assigns" the monitor profile to the values in real time so that the colors look like they should on the monitor. This is the simple explanation of course, there is much more going on in the background.
In the color management world there is only 2 options when you wish to play around with colors and profiles: assign or convert colors. When switching from one color space to another (i.e. from RGB to CMYK), your only option is convert since the laws of physics apply here. Within the same color space, if you assign profiles (or remove them, i.e. assigning nothing) you preserve the numbers while sacrificing (to various degrees) the appearance of the colors. When converting, you preserve the appearance of the colors while sacrificing the numbers in the file.
In your case, you need to convert the screen shot to a device-independent profile like Adobe RGB, or a device-dependent but easy to play with like sRGB. You can do that in Photoshop or Preview, as long as you do convert and not assign. Removing the profile is not really helping, since the numbers will have no meaning...
simply run shell command:
screencapture -i filename
this will start screencapture in interactive mode (selecting region). See screencapture -h
or man screencapture
If you realy need run the screencapture command from the applescript just use:
do shell script "screencapture -i filename"
you can test the applescript from shell:
osascript -e 'do shell script "screencapture -i /tmp/filename.png"'
Best Answer
Yes, this is possible.
You can use with Script Editor.app or Automator.app for your task. If you choose Automator.app, using the Run AppleScript action to embed your AppleScript snippets.
AppleScript: Simulating key presses
Take a look at using AppleScript to automate key presses, How do I automate a key press in AppleScript? An example from the top answer:
AppleScript: Capturing screen shots
To take a screen shot, there are numerous approaches. This question is a good starting point, Take a screen shot and save to desktop with current time as the name:
AppleScript: Mouse clicks
Simulating the mouse is trickier but likely possible, see Is there a way to simulate a mouse click anywhere on a screen in Dictate ?. AppleScript's GUI scripting is designed to interact with specific elements on the screen.
Aside: Copyright concerns
Please do not use this process to bypass copyright protection.