Merkel, according to your Spiegel reference said:
>Die Begrenzung der Restlaufzeit der deutschen Atomkraftwerke käme einer Vernichtung von volkswirtschaftlichem Vermögen gleich.
Which translates to
>Limiting the remaining service life of German nuclear power plants would be equal to destroying national economic assets.
So her concern was about shutting down existing nuclear power plants earlier than initially planned. She kept true to her word, and reversed that, only to re-reverse herself after Fukushima.
That's however not necessarily a very pro-nuclear stance, more a pro-"let them continue printing money with their existing plants because they have been good friends to the CDU in the past" stance.
What she didn't say however is that she favored investing in more nuclear power generation and nuclear technology in general.
New nuclear power plants were banned altogether. The agreement became law in 2002 (Atomgesetz). Angela Merkel, objected to the agreement, calling it a “destruction of national property” that would be revoked if the CDU came to power.
To be fair I only looked for 30 seconds and it is hardly a smoking gun to call not building nuclear power a destruction of national property as being 'pro nuclear'.