I don't think you have to worry about "upsetting the IP holders"; you can make a Halo mod featuring Big Bird and Carmen Sandiego if you wanted to, and I don't think they'd object to that choice.

If in your mod you portray the Friedens and the Koslovics as having originated from sassy 22nd-century hipster baristas that were violently arguing about Nickelback's role in music history, I really don't think you'd hear any knocks on your door from MS Legal -- my (considerably double-checked) understanding is that what matters is whether or not you're using the Halo IP for monetary purposes. How far off the beaten lore path you go with your content really isn't kept track of (the only possible exceptions I can think of to this would be if you did anything pornographic or similarly shocking with the Halo IP).

That said, I do get the feeling that we are going to be learning a little bit more about that period of history from 343. Whether in Halo 5: Guardians or in some other source, I don't know, but I've got a feeling. :)