They may have not offered any alternative theories for Western consumption, but their internal state media openly discuss a theory that it was shot down by an Ukrainian fighter plane.
The willingness of Russia's Government to state, with impressive conviction, the seemingly absurd is hardly unprecedented. "There are no Russian troops in Crimea" was once their mantra. Meanwhile rolls of film showing Russian troops, speaking Russian, wearing Russian uniforms driving Russian'-registered APCs were shown around the world.
As with so many of these tragic events, the most likely scenario is usually proved correct in time. Conspiracy theories simply don't have legs in the modern world where every hole in a theory is found and exposed. The chances of a Ukrainian fighter jet knowingly shooting down a civilian jet are a million to one. The odds of it being fanatical rebels probably more like two to one.