Inner product with homomorphic encryption
You can use these schemes instead: 


“Evaluating 2-DNF Formulas on Ciphertexts”, or
“A Simple BGN-type Cryptosystem from LWE”.


These schemes enable you to do addition, a single multiplication, and more additions. For inner product, that's all you need (encrypt each item separately, multiply pairs, and add all together).

Not everything needs FHE. In any case, somewhat HE would suffice since it's just a single multiplication.