\documentclass{article}
\usepackage{mathpartir}
\begin{document}

\newcommand{\testa}{
  This is the intended use:
  \begin{mathpar}
    \inferrule*{
      1\\
      2
    }{
      3
    }
  \end{mathpar}
}

\newcommand{\testb}{
  % LaTeX Error: \begin{mathpar} on input line 68 ended by \end{lines}. [\testb]
  But (because the code is generated), I have an environment in the rule:
  \newenvironment{lines}{}{}
  \begin{mathpar}
    \inferrule*{
      \begin{lines}
        1\\
        2
      \end{lines}
    }{
      3
    }
  \end{mathpar}
}

\newcommand{\testc}{
  If \textbackslash\textbackslash is renamed \textbackslash{}plop, it works (or well, the output isn't what is expected but I know how to fix it and at least it compiles):

  \newcommand{\plop}{\\\relax}
  \newenvironment{lines}{}{}
  \begin{mathpar}
    \inferrule*{
      \begin{lines}
        1\plop
        2
      \end{lines}
    }{
      3
    }
  \end{mathpar}
}

\newcommand{\testd}{
  % LaTeX Error: \begin{mathpar} on input line 70 ended by \end{lines}. [\testd]
  And it's not the \textbackslash{}relax that fixes it:
  \newenvironment{lines}{}{}
  \begin{mathpar}
    \inferrule*{
      \begin{lines}
        1\\\relax
        2
      \end{lines}
    }{
      3
    }
  \end{mathpar}
}

% Line 66
%\testa
\testb
%\testc
%\testd


\end{document}