Hi,
The class fancybox-iframe is meant for showing complete pages. So if you want to use fancybox-iframe and only show a contact form that is being generated on a seperate page, you will need to create a new template that does not show any header or other stuff and use that template for your contact page... More on creating custom page templates: http://codex.wordpress.org/Pages#Creating_Your_Own_Page_Templates
Another approach might be to include a hidden form inline. I do not know how WPMU Contact Form works (is that from WPMU.DEV? And how is that different from normal form plugins?) because I simply use Contact Form 7 on multi-site installations. But let's say:
1. your contact form plugin allows you to put a form in a sidebar as a widget and
2. your theme allows for a custom menu to be used as main menu,
then here is an example of how it might work for you:
1. Create your form as a widget that is available on EVERY (!) page and post. It does not matter where you place it (in the footer for example) because it will be hidden later.
2. Find out which ID or class name is used for the document object that WRAPS (!) your contact form. It can be a div or a ul or li. Then add a CSS rule to your themes stylesheet similar like this:
.widgets .your-form-widget-class {display:none}
3. Find out the ID of the form itself and link to it from your main custom menu with href/target #your-form-id and class fancybox (not fancybox-iframe)
You might need to be inventive to make it work with your particular theme and plugin...