When John writes that he saw the new heaven and earth he invisioned it having a new city which is called New Jerusalem. This of course is again after the Judgment of that Great city Mystery Babylon. I heard many interperations of this city, Rome, Russia, China and America, but really it's not that hard to understand that it's speaking of the flesh of Israel.
As to your proposal I think we should view the thousand years from when Christ ascended and begun sitting on the right hand of God casting satan [flesh] to the earth. In so they the flesh, woman, bondwoman begun to persectue the brethren. Again I refer to Acts chapter 8 this continues until the end of that age. Paul speaks about the Law which can't coexit with Grace in how he spoke of the bondwoman and the freewoman. So in this new earth and heaven there is no temple for God and Jesus are the temple.
Those thrones given to those martyrs where they reign with Christ in his throne. We see Jesus telling Peter that they held the keys of the kingdom to bind or loose. We also see them joining in Christ judgment upon those that killed them in the judgment of Jerusalem. There final act of judgment was upon the Whore Jerusalem where they through their faithful acts even in death where found clean and white not having been defiled by the flesh [bondwoman]. So needless to say the thousand years to me represent from Christ to the judgment of the Whore.