I think they should just lock people into a Covenant until they reach exalted with them, then allow them to pick another, rinse and repeat, while allowing them to switch freely between the one they currently have selected and any they already have exalted with; something like:
1st Covenant - Player is locked into it until exalted.
2nd Covenant - Player can switch between it and 1st Covenant, locked out of 3rd and 4th until 2nd is also exalted.
3rd Covenant - Player can switch between it, 1st and 2nd Covenant, only locked out of 4th until 3rd is exalted.
4th Covenant - Player can now switch freely between them all.
The fact is, there will be a lot of elitist min maxing nonsense forcing people into choosing specific ones if they want to do anything high end, so it would be better to work around that, while still having choices be relatively meaningful for awhile. Plus, you know they will be continuously tuning Covenants and Soulbinds as the expansion goes on. It would be pretty awful design to lock people into one that might start off good, but end up crappy later.