If the devs decide not to change the way game timers work by penalising you for having to log off, then I am certain they will lose a lot of players at some point in their playing career of this game.
I haven't met an MMO that doesn't have a penalty for failure to complete a mission/quest. I also haven't met one that doesn't have a timer on missions/quests. On those that are persistent world, of which there are a few, the timers keep going even after you log out.
This is just an argument to gain some aspect of a saved game, so there's far less risk in the game. It's the argument of the "I want my cake and eat it too" crowd.
This group of players are a minority, a vocal one, but a minority all the same.
FD is not going to change this core function of the game, for a minority. If this minority does leave, that's fine with everyone else, FD has your money, you have no grounds to gripe, because it's a choice, play as is, or leave.
No one is forcing you to do anything particular in game, you have choices, do missions, trade commodities, bounty hunt, pirate, explore, it's open to the player's imaginations.
If these player's leave, I certainly hope they find what they're looking for in life, but I suspect they won't, if they can't balance the various aspects of their lives, then they're going to find every single game out there, frustrating. They have no right to expect the game company's to give in to their demand's, because they are the minority, and that would hurt the majority.
I know there's going to be an argument that they aren't the minority, your argument on this too is invalid, you have no proof, so don't bother raising it, polls on forums are not going to work, because more players tend to play the game and read the forums, but fewer still actually take the time to post, or post regularly.