I thought you could choose either location, but seeing one of the designers responded I pulled the rules. Note Activate Disciple/Collect Standard Reward occurs in steps 3 and 4, THEN (if still possible) you shown that you meet the Bonus requirements.
When you complete a Mission you always do it in the following order:
1. Lay the Mission Card face up on the table
2. Show that you meet all Standard requirements
3. Activate your Disciple
4. Collect the Standard reward
5. (if possible) Show that you meet all Bonus requirements
6. (if possible) Collect the Bonus Reward
7. Place the Mission Card face down onto your “Completed Mission Card” pile next to your Clan board
I still thought that maybe there was some gray since earlier in the rules it notes you can activate from either location, but there is a nice little addendum just below the above section on the scoring mission cards page.
You must have a Disciple present at an Assignment space in each of the Dis- tricts shown on the Mission Card. (If a District is shown twice, you must have 2 Disciples in that District.) You activate one of the Disciples to complete the Mission (but it must be in a District shown in the Standard requirements).