Every time the eqgame.exe is changed, mq2 must be changed with it so yes you will have to wait till a new one is created. The great people here at redguides are always on top of this and do a fantastic job dealing with everything that sony has screwed up. Depending on how much sony screwed us up on this will reflect on how long it takes to fix mq2. Sometimes a couple days, sometimes a week or more.
As for the mm nerfs, it does not mean the reward is based off of how long it takes you to complete the mm. I believe it is a system they created based off of how long it has taken people to complete them since they have been out. I seriously doubt they would let the xp stay the same just for you sitting in the MM till the timer is up. Basically all the MM's that people wanted to do have all been nerfed in xp I am sure. People loved to do them because they were quick, easy, and great xp.
As with anything good in this game, it is only a matter of time before sony takes our advantages away from us, or at least try to. Now it's a matter of finding new exploits for us to terrorize LOL. There are alot of new missions coming in this expansion I think so I am sure people here will find lots of fun new stuff for us to do for crankin out the xp and rewards.