Ikael: the main issue with the Knot was the issue of so many characters journeying to visit Dany, and how it would sequence. He needed certain characters (Quentyn) to arrive first when she was in Mereen, and had to set up a way to get her out of the city and still have a compelling narrative there during the siege. I didn't like most of Dany's chapters in ADWD but all of Barriston's were great, and Martin has said that character is who helped him cut the Knot.
So now you have Dany away from the city, presumably about to conquer another khalasar and march back to Mereen. Meanwhile Tyrion is outside the city gates and Victarion is about to break the naval siege in the city's bay. Perhaps Marwyn will show up after the battle.
I actually like the general story arc, although I don't like the painstaking way he got there; many of Dany's chapters were extremely repetitive and could have been cut, perhaps in half. Dany will likely go back to the city and save it from the siege, but not before the "pale horse" overtakes much of the slaves she freed. Perhaps you're right about the pyramid being breached, thus further releasing the disease. Either way I think Mereen is fucked, and Dany may have to scorch the city in order to stop the spread. Which of course would only serve to make her seem even more dangerous to Westerosi lords, and would be an interesting parallel to what happened with the Mad King; in that case Jaime saved the city by preventing a Targaryen from burning a city, whereas Dany will have saved a city by burning it.