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Not sure if this is by design (or if I'm doing something utterly stupid), but I often create a ConfigParser object for my application and then pass this around (or make it global).
So when I do something like
 cfg.set("input_filter", "include_filtered", True)
and then 
 cfg.getboolean("input_filter", "include_filtered")
I receive an error (AttributeError: 'bool' object has no attribute 'lower').
Wouldn't it be more sensible if getboolean would return the raw value in case the raw value is already a boolean?
If not, which would be the best way forward for me?

In python3 you will get an error: "TypeError: option values must be strings". So, this is an infelicity in the configparser API. Or, rather, I presume it is a design decision (ie: python shouldn't guess what string format you want the value to have in the file).
I'll leave it up to Lukaz to decide if this should be closed, or if there is an acceptable feature request here. But your solution is to call str on your boolean values when you store them.

As R. David pointed out, this is fixed in Python 3 by emphasizing configparser is designed to hold strings at all times. Changing this would break lots of existing code out there. So, sadly, #wontfix.
Thank you for your report though. If you find the documentation is misleading, create a change for that and we'll submit it.