Hi! We're still working to improve this down the road, but for now you will have an option when you launch to bypass anticheat. This will allow you to play around with campaign and customs but not allow you to play any match made games. I highly suggest making a copy/backup of anything you modify so you'll be able to switch back and forth easily.
Commenter is a certified 343 employee.
I'm almost certain there would be a lot of people out there who aren't fully aware of how far MS is going to allow modding of these games. It is actually a big credit to them that they're even allowing this let alone embracing it so thoroughly and for that, I think they deserve some kudos.
tl;dr there are going to be mods in Halo, go buy it.