Workaround for align without using amsmath

I guess you mean the copernicus2.cls provided by the Biogeosciences. The files can be found on there website.

The class file loads the package txfonts which must be loaded after amsmath. The package txfonts has a mechanism to redefine some internal commands of amsmath which amsmath doesn't have.

You can load the package amsmath as follows to use align:

\RequirePackage[fleqn]{amsmath}
\mathindent0pt
\documentclass[journal abbreviation]{copernicus2}
\begin{document}
\begin{align}
1+1&=2 \\
    2&=2
\end{align}
Test
\[1+1=2\]
\end{document}

EDIT: Set option fleqn and mathindent=0pt

@Marco, amsmath does not load amssymb. The problem is two fold.

copernicus2.cls load txfonts.sty which define various \XintY macros which amsmath also define. Since amsmath define these using \newcommand the OP get an error because they are already defined.

This works

\documentclass[journal abbreviation]{copernicus2}
\let\iint\relax
\let\iiint\relax
\let\iiiint\relax
\let\idotsint\relax
\usepackage{amssymb,amsmath}
\begin{document}
\begin{align}
1+1&=2 \\
    2&=2
\end{align}
\end{document}

Though Marcos solution may be better, because the solution above may use a different font for those integral symbols than the Journal intended.