I've just made a try with my google's banner and it works fine! I've put my google's code after my Dokuwiki's code, in the sidebar.txt.
The only thing that I want to suggest you (if you want to put your ad in the sidebar) is to use a banner with width not greater than 160 px (for example 160x600 is a good choice).
For example:
* dokuwiki link 1
* ...
* dokuwiki link n
---
<HTML>
<script type="text/javascript">
/* <![CDATA[ */
document.write('<s'+'cript type="text/javascript" src="YOUR-PATH/js2.ad/size=160X600/r='+new Date().getTime()+'"><\/s'+'cript>');
/* ]]> */
</script>
</HTML>
----
Edit:
I want point out that my solution doesn't provide the use of googleads plugin. Simply allow html in your DW and than past the google code, between <HTML> tag, where you want to put your ads.
I've never used that plugin but, reading its section
https://www.dokuwiki.org/plugin:googleads#About, it seems to me that there some configuration that you need to set up.