I went about it the wrong way. I started off developing my mu live because I didn't think it would take off. Then it started to take off and now I have angry (rightly so) users that complain when I develop and test features. So I need to move the live install to a development environment.
Is it possible to just move the 'main' part of wordpress, develop it and test, and move back ONLY the main part into the live multisite install?
Yes, it is possible. BUT NOT ADVISED!!
All blogs in your database have a unique prefix.
So if your main site has the tables with a prefix like wp_ then the tables of the site with ID=2 will have a prefix like wp_2_.
To move the main site only, you'd have to copy the main site tables from the db.
My advise would be to simply download your entire database on your dev server and develop normally. This is something that will only have to be done once, so it's not a big deal.
You can then develop your code and upload it on your live server. You won't need to upload the database since all your changes should be in-code.