Hey Kristof,
In compojoomComment 4.1 the comments were outputted onPrepareContent. This means:
the plugin gets the article $row and we attach the comments to the end of it. This is all good, but in a lot of cases we get conflicts with plugins that are also executed onPrepareContent - the best example is the e-mail cloaking plugin. It was transforming the emails in the comment form...
Since the onPrepareContent event is used to make changes to the article and since we don't do any changes to the article the best event for the comments is onAfterContent... And compojoomComment 4.2 does exactly this.
Now with your specific template the onAfterContent event is displayed way below after your article. What you need to do is a template override and move the <?php echo $this->onAfterContent; ?> tag to the place where you want the write comment to be.
Cheers,
Daniel