On the contrary - I think he gets it completely. If our rights come from either our Creator or from our nature, then they are truly "inalienable". This means that our rights cannot be taken away and that they precede any form of social organization.
To collectivists generally (and Obama specifically), rights come from the government, meaning they are subject to the will, intentions and needs of others. I believe Obama's continued use of the word "inalienable" is gratuitous; he either does not understand what it truly means, or more likely uses it for rhetorical effect.
Yes he does. Leaving GOD out, and substituting 'inalienable' was no mistake.