I'm pretty certain the timid creature grinders will be going away soon. If so, it will be clear it was an exploit. If they're still here 2-3 months from now, then I guess we can consider them fair game.
I do agree that scaling mission rewards would do a lot to help this problem. One two hour mission should provide rewards equal to four 30 minute missions, and so on.
The current reward system was designed in a way that this was bound to happen. The short grind missions were the obvious replacement for the clickies under the new rules. There are enough people who just want to gather resources as quickly as possible, that they'll always default to whatever comes easiest. The only good thing about the clickies is that people at least had the decency not to rate them up, probably because they were pretty clearly an exploit and having them at the top of the list would just bring more attention to them.
At this point I'd say we don't even know whether people really want grind more than story, because it's not a level playing field. The reward/time is stacked so much more in favor of shorter missions, that they'll dominate simply based on that.
That being said, I think that different categories is still necessary so it's easier for people to find what they want. The whole search tool is not enough. There is too much inertia involved in people using the search. You need a quick list that draws them in, and once they feel there is worthwhile content for them, then they'll eventually learn how to use the search.
Also, if the Foundry really is about story, something needs to be done to encourage that. In addition to the featured missions, which are pretty rare as only one is added per week, maybe when Branflakes plays through missions to see if they qualify for the feature, he can also tag them as being "story qualified" (whether good or bad), which means they would qualify for an extra reward. Even if that's kind of subjective, at least it would help try to throw a bone to story authors. If that's really what the Foundry is supposed to be about, then I don't see why it's unreasonable.