I've created an update site for my plugin using this tutorial. My update site works perfectly fine when installing from the folder, but when I put it into a zip and try to install "from archive", eclipse seems to treat it as a jar file.
Is there an option to correctly distribute a plugin as zip file?
It looks like you are creating an old-style update site (ie- pre- Eclipse 3.4 using site.xml and not using p2).
You need to generate p2 metadata for your update site. Take a look at this tutorial for the simplest way to create a p2-aware update site:
http://www.vogella.com/articles/EclipseP2Update/article.html
p2 is the Eclipse provisioning system and it is the component that is used to find and install plugins and features into Eclipse.