I'm 100% on board with pony Indiana Jones writing about her adventures and most ponies thinking the books are fiction; I think that's a pretty good concept that fits in just fine with what we've seen before.
That said, I think the execution of it here was a little off. Why does Daring Do dare to do what Daring Do does? Indiana Jones is an archaeologist; he does field work and happens to run into evil cults and Nazis and the like. Daring Do is... a hermit? Why is she the one doing battle with the monkey thing? If he's really got major evil plans with global implications, surely some of the Princesses should be aware of this. You can suppose that there's a lot more going on in the background here, but it would have been nice to have some line about the author being in the crown's employ or that they actually had to go halfway around the world to find her or something.
The other thing that really hurt the episode for me was the main cast's uselessness. Twilight in particular deserves a lot of blame here. This episode was notable for being (I think) the first time we saw significant pony-on-pony violence (changelings don't count and you know it). And the main cast just watched the fight. Now, I understand Fluttershy and Rarity not charging right in, but Applejack? Even Rainbow Dash. And in the episode just before this we saw Twilight (apparently effortlessly) immobilize four resisting ponies simultaneously, including freezing a pegasus in mid-flight and a pony running around in a panic. She really dropped the ball letting the thugs get away.
Edit: I haven't weighed in on Castle Mane-ia either, I guess. I'm less positive than some here, I suppose. Moment to moment it was fine, but I had issues with the premise. So basically the reverse of my take on the most recent episode. It was really hard to buy that suddenly everyone wanted to go to the castle that as far as we knew no one had even heard of before the season opener (it didn't seem to be the case that they wanted to go there /because/ they had all just found out about it, other than Twilight). Plus it's in the middle of the forest that ponies typically only go into for very good reason and which scares them.