I fully realize that CoreOS is meant to be mostly immutable so that nothing is installed in the userspace. And for 99% of the use-cases I agree. I'm using CoreOS/toolbox when I need to get some actual work done but I also need to slightly update the user environment so that I can properly Docker-ify my development environment.
The .bashrc is a symlink to a read-only file. All you need to do is:
cd $HOME
rm .bashrc
cp /usr/share/skel/.bashrc .
Hope that helps.
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