He said he was not aware that any of the companies were already engaged in illegal activity at the time that he helped to set up them.
My guess: The author or the copyeditor was enforcing some (entirely spurious) rule against splitting an idiom such as “set up,” and as a result replaced a perfectly normal construction (“set them up”) with a weird and jarring one. I wouldn’t go so far as to say that “set up them” is ungrammatical; it’s as grammatical as “set up the companies” would be. But it is surely unidiomatic, as a Google Fight reveals; a search through Google News shows an even more lopsided tally, 200:1 in favor of “set them up” rather than 20:1. I’m with Horace‘s view that custom is the test of good usage, and “set them up” is customary.
Maybe I’m wrong, and maybe “set up them” was just a spontaneous error. But to me it smacks of a general splitophobia, raised to a new level.
UPDATE: Some commenters suggested the problem might be an attempt to avoid a preposition at the end of a sentence; that might be.
On the other hand, Mark Liberman (Language Log), who’s a real linguist, did what real scholars do — which is to say some research. His conclusion, based on the Sun‘s and others’ past practices: “The sentence that Eugene Volokh found is probably an inadvertent editorial error, not a mistaken editorial choice.” He also says (as does his colleague Bill Poser) that,
“… helped to set up them” (with the relevant structure and interpretation) really is ungrammatical, i.e. well outside the norms of contemporary English, not just (as Eugene suggested) “unidiomatic”. The only (marginal) exception, I think, would be cases with contrastive stress on the pronoun, e.g. “First we’ll set up YOU, and then we’ll set up THEM”.
I happily defer to the view of experts here, especially since they are experts whose work I’ve long admired.