I'm not sure what the motivation for killing him and continuing to pretend that he's alive would be, but then again, I don't understand most conspiracy theories.
Do you really think the Ecuadorean embassy, which had to install a shower so they could house him, is able to resist political pressure from basically all of NATO? Snowden had to flee to Russia, not even a Russian embassy, and he's not even leaking anything new. (I'm not necessarily claiming that anyone is actively manipulating WikiLeaks, just that there are a million easier ways to do it than secretly killing him and making a CGI double - and secretly killing him would require Ecuador's cooperation, anyway.)
I don't think it's a very popular conspiracy theory that Obama would have killed him. Just a few people who remember SECSTATE Clinton talking about droning him, and that has given them fuel for this speculation.