I have completely different idea.
What about Clan Confederations instead of Alliances.
Here is how it would work:

Clans cannot freely choose allies on their clan panel.
Instead, they have two options:
1.They can create a confederation with another clan that does not belong to any other confederation).
2.They can join a confederation of two clans in which there is room for a third (we assume a limit of 3 clans per confederation.
Once they have joined a confederation, they cannot wage war against clans belonging to this confederation.
Clans in such a confederation can wage war together against other confederations and against non-affiliated clans (clans not belonging to any confederation).

I did a little comparison in paint.

Bonus idea:
Clans in the confederation can actually fight with each other but it's not a war just a "friendly skirmish" or something like that.
Clans get less activity points for a friendly skirmish than they would get for a war with a clan from outside the confederation.
Normal wars points are capped at 15 pts max, calculated as warsPlayed / 7 * 15 .
War points from Friendly skirmishes would be capped at 8 pts max, calculated as SkirmishesPlayed / 5 * 8
So you will receive 8 points for the first 5 skirmishes fought with friends from your confederation in a given month.

It is therefore a kind of war geared more towards having fun together and slightly improving clan activity than towards competition and profit.
It's been a long time since I've fought wars but if I remember correctly you can set up some sort of war reward, right?
In skirmishes you wouldn't have that option.