No, I haven't read any of the Barry Eisler John Rain books. But did read the Killing Floor.
Two things. First of all, if a treasury agent, which I assume to be a member of the Secret Service, was murdered and it was brought to the attention of his superiors, there would be other agents all over the area to investigate.
Spoiler info.
When Reacher was first in the warehouse and looking at the stacks and stacks of money, my first thought was, they're going to burn it all up. And so they did. lol
All in all, in spite of the minor flaws, I did enjoy the book and am now reading the second one Die Trying.