I've been searching through "The History of the Lord of the Rings" (by Christopher Tolkien) trying to find out how JRRT decided to have Aragorn go after Merry and Pippin instead of following Frodo. So far I haven't found any debate about it. I'll keep looking in "The History..." and in "The Letters" to see if I can find out.
What's interesting to me is that in earlier drafts when the Fellowship breaks, the orcs aren't there. Merry and Pippin just get lost and wander into Fanghorn and Treebeard. Legolas and Gimli head north (back home?) and in one version are captured by Saruman and in another meet Gandalf. Boromir doesn't die and he and Aragorn go to Minas Tirith where Boromir becomes jealous of Aragorn, falls further into evil, and does a Wormtongue. Poor Boromir! I'm glad in the end that he "kept his honor".
Off to more research!
The raid/trap by the Orcs was perfect because the fog of war (along with the personal crisis of Frodo) created a situation of total chaos, where no one knew where anyone was. And so off they went in many directions. It's interesting that he thought of discarding Legolas and Gimli at this point (by sending them off back home) -- of all the Fellowship (maybe even including the now dead Boromir), from this point forward they have the least "book time". They play a significant role in the battle at Helm's Deep, but are riders-along for much of the rest of the tome. Perhaps he thought of "sending them home" because from that point forward in the story plan he didn't really have anything coming for them but bit parts -- and perhaps those bit parts were added to or embellished later on in the story to justify keeping them along.