I'm not an expert in this area, but since homomorphic encryption exists (though is still impractical) and obfuscators do not exist (http://www.iacr.org/archive/crypto2001/21390001.pdf), it follows that the former can't be used to construct the latter.
Currently homomorphic encryption is extremely limited and/or computationally expensive.
The most efficient approaches let you do only one type of operation, which isn't sufficient for arbitrary code execution. Known approaches that allow general operations are expensive (if they are secure). See https://secure.wikimedia.org/wikipedia/en/wiki/Homomorphic_e...