First off, PyPy uses a JIT, so there's no obvious reason why it would have to be slower than 'optimized SIMD code' (whatever that is). The actual performance all depends on the quality of the JIT and the quality of the input into the JIT.
Second, they clearly state in the blog post that the PyPy version of the algorithm is easier to write than the equivalent C++, because the JIT can transform their polymorphic Python into efficient native code - doing the same with C++ would require the use of template expansion or a code generator.
Third, if the idea of sacrificing a tiny amount of performance in order to reduce the cost of development and maintenance is that abhorrent to you, Python is almost certainly Not For You.