(Your post popped up in my twitter feed)
I'm not sure why you said you needed to one-hot encode categorical variables for scikit's random forest; I'm fairly certain you do not need to(and probably shouldn't). It's been awhile since I looked at the source, but I'm pretty sure it handles categorical variables encoded as a single vector of numbers just fine from empirical tests; performance is almost always worse if the features were one-hot encoded.