A preliminary attempt at calculating rep points as a function of time spent.
Missions listed in order of time taken to complete them. Mission completion times include the time required to travel to a dungeon/zone or mission trigger of some sort. I'm a little unsure about the time for the last 5 missions as I didn't pay close attention to the clock when doing them.
A Time for Heroes: 3 mins
Curse of the Nornbear: 10 mins
Assault on the Stronghold: 12 mins
Against the Charr: 13 mins
GOLEM: 20 mins
A Gate too far: 20 mins
Blood Washes Blood: 25 mins
Finding the Bloodstone: 35 mins
The Elusive Golemancer: 45 mins
Warband of Brothers: 55 mins
Destructions Depths: 65 mins
The first three missions take 25 mins total and yield 3k rep.
3 Missions: 3000/25 = 120 Points Per Minute (henceforth PPM)
4 Missions: 4500/38 = 118.4 PPM
5 Missions: 6000/58 = 103.4 PPM
6 Missions: 9000/78 = 115.4 PPM
7 Missions: 12000/103 = 116.5 PPM
8 Missions: 15000/138 = 108.7 PPM
9 Missions: 18000/183 = 98.4 PPM
10 Missions: 22500/238 = 94.5 PPM
11 Missions: 30000/303 = 99 PPM
Returns seem to diminish after the first 3 missions. Although, the returns stay pretty constant up to the first 7 missions. Thus, it appears that the optimal number of missions is 3, 4, 6, or 7.
If all 11 missions can be completed in 250 minutes, you would have a PPM of 120. As I said, I'm not 100% certain about my times on the last 5 missions but I feel like the times listed are pretty close to what it took me.
Given the greater chances of wiping or getting slowed down due to deaths on the longer missions, the safest and most consistent method would be to keep doing the first 3 missions. The third mission may be Assault on the Stronghold or Against the Charr depending on the player.
More estimates on time to complete the missions are welcome.
Edit: I'm doing these missions again using a stopwatch and finding that my numbers in this post are exceedingly high. So ignore the calculations herein. Look further down in the thread for more reliable numbers.