No, entanglement decay does not violate the second law of thermodynamics.
To understand what is going on, consider a quantum system which is initially in some pure state which might or might not be entangled.
Let us now couple this system to a environment, which e.g. forms a thermal reservior. Then, after a while, the system will be in a thermal state
$$
\rho \propto e^{-\beta H}\ .
$$
This is, the system will be in a mixture of energy eigenstates $|\psi_i\rangle$ of the system with a corresponding weight $e^{-\beta E_i}$.
The scenario here is therefore very different to the question you linked to (which talks about the entanglement of a randomly drawn pure state): Here, we don't have a known pure state drawn from some distribution -- which indeed would be entangled with high probability -- but an ensemble. Now the point is that even if the individual pure states in an ensemble are entangled (which is very likely following the linked question), this does not at all have to be true for their mixture!
To understand why this is the case, consider e.g. the four Bell states
\begin{align}
|\Phi^\pm\rangle &= \tfrac{1}{\sqrt{2}}(|00\rangle\pm|11\rangle)\\
|\Psi^\pm\rangle &= \tfrac{1}{\sqrt{2}}(|01\rangle\pm|01\rangle)\ .
\end{align}
They are all maximally entangled. However, an equal weight mixture of the four Bell states is the maximally mixed state, which can equally well be understood as a mixture of four product states $|00\rangle$,
$|01\rangle$,
$|10\rangle$, and
$|11\rangle$ -- this is, the mixed state is unentangled (as it can be constructed without using any entanglement). (More generally, any mixture where none of the four Bell states has a weight $>1/2$ is unentangled.)
Thus, there is no contradiction to the second law: While thermalization indeed goes "from one to many", and almost all pure states are entangled, many pure states together (i.e., an ensemble of many pure states) do not need to be entangled (and indeed such a mixed state is unentangled with a significant probability).