First off, I think that people take the game too far when they thing an optional thing is "mandatory" for progression. Blizzard has always stated that the coins, mogu runes, etc are all optional to give you an extra chance at loot. Loot works exactly like it did in every other expansion, it drops, and you can roll on it, use DKP, loot council etc.
If people feel that it is now "mandatory" and part of core game play to have coins each week (which its absolutely not, and is completely optional game play), the should just take out the coin system.
Removing bonus rolls from normal and heroic raids would do two things:
1) Would greatly reduce the QQ about dailies being mandatory
2) Would bring the indented purpose of the bonus rolls closer in line with how the developers wanted them to work
Keep it for LFR so those people can feel good to try to get more loot. The real raiders in normal and hardmode wont have to bother with the system. It just feels too clunky, and a lame way of providing more "content" by way of dailies, and other "get you out in the world" type activities.