The Shadowlords have been defeated, so it would make sense for that group to disband.
Minax has been MIA for a very long time, so it would make sense for her forces to disband.
Lord British has been MIA for even longer than Minax... but with the recent victories their moral should still be strong enough to stick together.
CoM lost their home town... but that is supposed to get re-built.
If I knew for a fact that only one faction was going away, and the other three were staying... I'd say Shadowlords is the most likely to disappear (with either Minax returning, or a new super-villain taking her place to lead the Minax faction).
The whole facet has been in flux for years though, and the followers of each group have rarely actually acted in a way that represents the reasoning behind the formation of the factions... so I most expect all four factions going away, and three new ones forming.
Either...
Order, Chaos, and Balance.
or
Virtue, Anti-Virtue, and Armageddon.
Hopefully with an introduction of some game mechanic that encourages members in each group to act based on the principles behind the faction (even if it is as simple as having the decor of faction cities change based on who controls it, and how long they control it).