I ended up rebuilding my entire airline to get around this.
Started with a base in A with the intention to make B a hub as well. Started with a route from A to C, made C a hub. Opened a route from C to B, then made B a hub. Deleted the hub at C (it was just temporary anyway) and also deleted the route from A to C. Now I have A and B both hubs but with no flight in between them. C was a temporary hub, but is now completely unserved.
I could start a route from B to A if I wanted, but actually I'm fine like this. However this should have been so much simpler.
Also it requires to have at least 30 reputation in order to have 3 hubs (A, B and C) even if you only need 2 hubs (A and B). Can't do this trick if your reputation is less than 30.