Earlier quoted context omitted.
Homomorphic programs are designed to run without knowledge of the key. You have to process every piece of data in basically the same way. So I'm not entirely sure where you think the side-channel attack would arise.
because the simple fact you can process the data and examine the output reveals untold quantities of information about the key. the known plaintext attack breaks pretty much every crypto system, mix that with statistical analysis of this "processing" and I'm sure whatever is in the cloud will surrender its secrets pretty quick. And all that risk for what benefit? none of this processing will ever be faster than doing…
The benefit comes into play when you mix data from different sources that don't trust each other (to the point where they would never agree to one of them doing the processing in place). Homomorphic encryption allows combining the data without ever revealing it to the one doing the computation.