...And yet, all I can think is "the Kingpin, what an idiot."
That Tom was extremely loyal and clearly extremely competent (it's implied that he has been working for Kingpin for a long time, handling important tasks, without ever screwing up until now). Killing him off because of one mistake seems like an incredible waste of precious resources.
I understand the importance of letting underlings know, in no uncertain terms, that they must not screw up or they will pay dearly. So, of course, examples must be made. But even so, considering how rare extremely loyal and extremely competent underling seem to be, killing them off like that still seems like a real waste.