Addressing a few anti-Marienburg arguments:
'Second Fleet is fine for protecting the coast we do have' is an equivalent argument to 'One shoe is fine given the other foot got hacked off'. Though, to fully complete the metaphor, it would be more along the lines of, 'One shoe is fine given the other foot got hacked off, also the person who hacked it off has a monopoly on prosthetics and won't lower the prices so we can replace it and also threatens to hack off the second foot if we look into developing another prosthetics source'. You could almost make an argument for tariffs being Marienburg's right as a sovereign state that just happens to sit on the only safe northern port, until you got to the part where they directly sabotage any attempt to build a second safe one.
'Marienburg won't be so bad now we have the canal', also doesn't recognize the point - opening the Sea of Claws is about more than opening trade in that direction and it's been said over and over again; it's about protecting more or less then entire north Empire (also, the canal doesn't directly benefit Kislev, and protecting the Sea of Claws would).
'Marienburg's ability to pressure the Empire isn't that big or that predacious' - multiple dwarven kings collaboratively decided to open trade at the absolute opposite end of the Empire with the canal, and according to Bitternach, even a temporary embargo by Marienburg was enough to do 'unacceptable things to the budget'; to the point that Bitternach's go-to attitude about the canal until Mathilde corrected him was to ask if she could convince them to stop it. Yes it is that big, and yes they are that absolutely predacious - Marienburg has an effective monopoly on trade tariffs for the Empire and is willing to fuck over anyone, anywhere to keep it, including the entirety of Eight Peaks and the Karaz Ankor on the other side of the world.
Arkat Fooger becoming its leader might help things slightly - it might also change exactly nothing, as he's an elected leader beholden to the Staadtsrad. Marienburg's policy is monopoly at all costs, and I doubt a dwarf leading it (who is hardly considered part of the Karaz Ankor proper at all) is going to change that.
Any sort of argument about Marienburg's 'rightful sovereignty' should do well to remember that it wasn't some righteous stand against the tyranny of the Empire - it was first made an electorate by our best emperor (Magnus the Pious) to avoid a succession crisis and civil war to claim it, and then sold off by our shittiest emperor (Luitpold) piece by piece until it was vulnerable enough for them to secede. The Marienburg oligarchs and electorate literally bought the rights to maintain the Imperial Fleet and then siphoned it into their own private navies, embezzled enough taxes until they had a war chest and then seceded when the Empire would be least able to respond.
This is all to say, the Marienburg problem, unlike the Waystone problem, is immediate and will always be immediate until we stop it from being able to explode whenever their merchant princes decide it is most profitable to do so, with zero regard for the knock on consequences to the world at large - which it does frequently, and to a certain degree, constantly.