The time taken for that would be more than it would take to get it via dailies. It would lead to burn out just like reputations did. I'm not sure how many charms you can get if you do all the dailies in mop at present (I would guess if you unlocked all of the dailies you can get the cap?)
Say you can get 90 charms from doing all the dailies present you would have to have them unlocked to begin with as most are locked behind golden lotus etc. So you would have to balance it around that.
I would put a limit on there so heroic dungeon runs are NOT the defacto best route to take for getting charms. getting 5 charms per run and a limit to how many you get per day makes it an optional way of getting charms. This way you have a balance between the two. You could adjust the number for sure as thats just an example but I would not be in favour of getting charms for doing dungeon runs as then you sideline the daily quests which unlock important story elements.