It definitely is. Church Turing thesis basically states that all systematic procedures can be encoded as math. So, software can be encoded as math yes, but also music can be encoded as math. Life can be encoded as math (which is what our DNA is).
Rather than providing a basis of not allowing software to patented, I think it makes the statement "X can be encoded as math" trivially true - and therefore uninteresting.
In so far as there is value in patents on any systematic procedure at all, the position that "software should not be patentable because it can be encoded as math" is completely untenable.