Here's a question, at what point in the MQ would the least amount of gates be opened?
The answer (zero) is at two points in the quest line. The first instance is just after the Kvatch gate is closed, and the other time is at the end of the Main Quest.
If you close the Kvatch gate, and never talk to Martin (you can do the whole battle for Kvatch if you want), you get one sigil stone, a couple of fame points, and no further worries about the Oblivion Crisis.