You need to customise the ItemStyle XSL for the CQWP, and manually tie your CQWP webpart instance to your customised ItemStyle. You will also need to add WorkspaceLink to the CommonViewFields property in the webpart instance.
When you're editing the ItemStyle, you should be able to simply do this:
<xsl:value-of select="@WorkspaceLink" />
To get the url to the Workspace.
So, step by step:
Add a CQWP to your page and wire it up to the list.
Export it (so it downloads as a .webpart file).
Add WorkspaceLink to CommonViewFields.
Copy ItemStyle.xsl in the site's Style Library and rename it to something like MyItemStyle.xsl.
Make the changes in the appropriate itemstyle template such that it renders your workspace link.
Upload your customised ITemSyle to the Style Library.
Go back to the .webpart file and modify the ItemStyleLink property so that it points to your new itemstyle file in the style library.
Import your edited CQWP webpart file into your page and add it.
Have a Google around for "Customising Content Query Web Parts", "customising ItemStyle" and "CommonViewFields Content Query Web Part" for more info.