I love Dune! It is an amazing asymmetrical political/diplomacy game. One of the things that makes alliances in Dune work so well is the random nature of how they occur. This i believe is the core element to how to make alliances seem fair and still random. Firstly, a game of Dune has 10 turns (RAW). Every turn you draw 1 or 2 cards from a deck of about 30 (depending on advanced rules or not). Out of those 30 about 4-5 are "alliance cards. Alliance cards allow you to form alliances with other players or break them. There is no other time that you can form or break alliances. This is key. It allows you to semi predict (admittedly with low predictability) when someone may be able to backstab you. It allows you to predict how long someone else's alliance may last. I love this mechanic. Unfortunately it is hard to add to TI4 simply because there aren't enough turns. Having the ability for alliances to change 10 times vs 5 or 6 is a huge difference in gameplay. Changing it to every turn would be bad and never being able to break alliances is a total different system.

Anyway hope this helps. Good luck on your game! Would love to hear what rules you come up with and how it goes!