In your example, you don't use the correct encoding for the Libertine font.
Here's an example which uses Cochineal with the greek letters from Libertine. The code which declares the greek letters is based on newtxmath
's code.
\documentclass{article}
\usepackage{cochineal}
\usepackage[cochineal]{newtxmath}
\makeatletter
\newif\iflibus@sansmath
\makeatother
\DeclareFontEncoding{LS1}{}{}
\DeclareFontSubstitution{LS1}{libertinust1math}{m}{n}
\DeclareSymbolFont{LettersLibertinus} {LS1}{libertinust1math}{m}{it}
\DeclareSymbolFont{OperatorsLibertinus} {LS1}{libertinust1math}{m} {n}
\DeclareMathSymbol{\Gamma} {\mathalpha}{OperatorsLibertinus}{"00}
\DeclareMathSymbol{\Delta} {\mathalpha}{OperatorsLibertinus}{"01}
\DeclareMathSymbol{\Theta} {\mathalpha}{OperatorsLibertinus}{"02}
\DeclareMathSymbol{\Lambda} {\mathalpha}{OperatorsLibertinus}{"03}
\DeclareMathSymbol{\Xi} {\mathalpha}{OperatorsLibertinus}{"04}
\DeclareMathSymbol{\Pi} {\mathalpha}{OperatorsLibertinus}{"05}
\DeclareMathSymbol{\Sigma} {\mathalpha}{OperatorsLibertinus}{"06}
\DeclareMathSymbol{\Upsilon} {\mathalpha}{OperatorsLibertinus}{"07}
\DeclareMathSymbol{\Phi} {\mathalpha}{OperatorsLibertinus}{"08}
\DeclareMathSymbol{\Psi} {\mathalpha}{OperatorsLibertinus}{"09}
\DeclareMathSymbol{\Omega} {\mathalpha}{OperatorsLibertinus}{"0A}
\DeclareMathSymbol{\alpha} {\mathalpha}{LettersLibertinus} {"0B}
\DeclareMathSymbol{\beta} {\mathalpha}{LettersLibertinus} {"0C}
\DeclareMathSymbol{\gamma} {\mathalpha}{LettersLibertinus} {"0D}
\DeclareMathSymbol{\delta} {\mathalpha}{LettersLibertinus} {"0E}
\DeclareMathSymbol{\epsilon} {\mathalpha}{LettersLibertinus} {"0F}
\DeclareMathSymbol{\zeta} {\mathalpha}{LettersLibertinus} {"10}
\DeclareMathSymbol{\eta} {\mathalpha}{LettersLibertinus} {"11}
\DeclareMathSymbol{\theta} {\mathalpha}{LettersLibertinus} {"12}
\DeclareMathSymbol{\iota} {\mathalpha}{LettersLibertinus} {"13}
\DeclareMathSymbol{\kappa} {\mathalpha}{LettersLibertinus} {"14}
\DeclareMathSymbol{\lambda} {\mathalpha}{LettersLibertinus} {"15}
\DeclareMathSymbol{\mu} {\mathalpha}{LettersLibertinus} {"16}
\DeclareMathSymbol{\nu} {\mathalpha}{LettersLibertinus} {"17}
\DeclareMathSymbol{\xi} {\mathalpha}{LettersLibertinus} {"18}
\DeclareMathSymbol{\pi} {\mathalpha}{LettersLibertinus} {"19}
\DeclareMathSymbol{\rho} {\mathalpha}{LettersLibertinus} {"1A}
\DeclareMathSymbol{\sigma} {\mathalpha}{LettersLibertinus} {"1B}
\DeclareMathSymbol{\tau} {\mathalpha}{LettersLibertinus} {"1C}
\DeclareMathSymbol{\upsilon} {\mathalpha}{LettersLibertinus} {"1D}
\DeclareMathSymbol{\phi} {\mathalpha}{LettersLibertinus} {"1E}
\DeclareMathSymbol{\chi} {\mathalpha}{LettersLibertinus} {"1F}
\DeclareMathSymbol{\psi} {\mathalpha}{LettersLibertinus} {"20}
\DeclareMathSymbol{\omega} {\mathalpha}{LettersLibertinus} {"21}
\DeclareMathSymbol{\varepsilon}{\mathalpha}{LettersLibertinus} {"22}
\DeclareMathSymbol{\vartheta} {\mathalpha}{LettersLibertinus} {"23}
\DeclareMathSymbol{\varpi} {\mathalpha}{LettersLibertinus} {"24}
\DeclareMathSymbol{\varphi} {\mathalpha}{LettersLibertinus} {"27}
\begin{document}
\[
\alpha\beta\gamma\delta\epsilon
\varepsilon\zeta\theta\vartheta\eta\iota
\kappa\lambda\mu\nu\xi
\pi\varpi\rho\sigma\tau\upsilon
\phi\varphi\chi\psi\omega
\Gamma\Delta\Theta\Lambda\Xi\Pi\Sigma\Phi\Psi\Omega
\]
\end{document}

To compare, here's the same example without the new definitions of greek letters.
\documentclass{article}
\usepackage{cochineal}
\usepackage[cochineal]{newtxmath}
\begin{document}
\[
\alpha\beta\gamma\delta\epsilon
\varepsilon\zeta\theta\vartheta\eta\iota
\kappa\lambda\mu\nu\xi
\pi\varpi\rho\sigma\tau\upsilon
\phi\varphi\chi\psi\omega
\Gamma\Delta\Theta\Lambda\Xi\Pi\Sigma\Phi\Psi\Omega
\]
\end{document}
