While I don't think that looping through a given level repeatedly should be encouraged, what you propose is easy enough to work around. Player A has a group at content that players A and B want to loop through. Player B joins player A's group. Player A then goes through the level, and goes up to Haven at the end. Then player A joins player B's group and goes solo. Player B now completes the level and goes up to Haven at the end, and joins Player A's group. He can join player A's group again because it's a different group from what player A did before, as player A's original group finished the level and disbanded.

I guess that what you propose is progress of sorts, as it does require players taking turns looping through, rather than letting one character anchor for a bunch at once. But it's not that much progress, as all it means is that who anchors the group has to rotate.

I had a possible idea where a player who goes solo will be banned from the previous instance, and have that ban list be inherited by all clones of the parent instance. The player that invoked go solo would have to be granted an exception, and be labeled the "Foster" for that cloned instance (more below).

There are 2 flaws with this idea. First, if the player suffers a disconnect that results in him being dropped from the party, he can't rejoin due to the ban list. Second, it doesn't stop an anchor from chaining multiple clones. In order to close the loop holes, the server would have to enforce 3 rules.

1. The Foster is allowed exception from the instance's ban list. This allows the player to join an instance he invoked, but can't join other clones of that instance due to the ban list.
2. A player can NOT invoke go solo in an instance where he is the Foster. (stop chaining)
3. A cloned instance should never be more then 2 generations from the grand parent.

Rule 1 allows go solo to function while preventing him from rejoining future clones due to the ban list (closes one loop).
Rule 2 prevents a player from invoking multiple clones.
Rule 3 serves 2 purposes. First to prevent a foster in one branch of clones from jumping to the other branch and continuing it there. Second, to reduce decay that's somehow inherent with the cloning process*. Given how rarely this option is used in normal gameplay, I don't foresee any major game stopping issues.

*If an instance is cloned enough times, it starts encountering glitches and break downs like the shield bug.