Incentive works much, much better than punishment for altering behavior.
If speed runs of AK stop being viable because of a mechanics change and the only reason to kill trash is because you have to, most people will stop doing AK entirely. It's just not worth the time for a bunch of ilvl 60 greens and some tomes if each run is going to take 60-90 minutes and you'll rack up a massive repair bill in the process. The 8 man story dungeons become more efficient, from both time and cost perspectives, if you have to slow-run AK.
If speed runs of AK stop being worthwhile because you get something of sufficient value from the trash, people will start killing the trash.
Edit: And in a wider sense, if your goal is to create a healthy, thriving MMO, punishing players is a generally stupid idea. If people do something unanticipated (FATE parties, AK speed runs) and the devs' response is to punish people, those players won't feel valued and are likely to quit. It's bad business sense on SE's part to just nerf nerf nerf. If something is exceptionally unbalanced to the point of breaking the game (e.g. finding an exploit that triples tomes dropped in a run), that obviously needs to be addressed.
It's a much better business decision for SE to learn from their mistakes, avoid repeating them in the future, and generally let things stand for the time being (or create incentive to alter behavior). Nerfing FATE XP or adding mechanics to prevent speed running is foolhardy. Especially 2 weeks into a game's life. Add daily quests that give a big chunk of XP for completion of a dungeon, and you'll see people migrate towards the DF and mostly the hardcore grinders will stick to FATEs. Add drops of value to AK trash so that people want to kill it. You lose money hand over fist just by being 50 and doing content, and rather than introducing money through dailies, add it through trash (which is also an effective time gate).