With this kind of thinking, one could claim that there are still WMD in Iraq. No one has found evidence of WMD, and, like UFCo's possible direct involvement in the '54 overthrow, few published scholars believe it. But Hussein had shown an inclination to obtain them before and he had a motive to do so, thus, for you to be logically consistent, your idea of "intent" should lead you claim that they must be there, despite any solid evidence in support.
A historian is irresponsible to claim something as a fact without evidence, despite his or her personal feelings that it may have existed. The best that you and I can say is this: "UFCo may have directly colluded with the US government in overthrowing Arbenz (and leading to decades of death and instability in Guatemala), but no one has yet found direct evidence of this (yet)." To say "UFCO directly colluded with the US government in overthrowing the Arbenz government because they had a motive to do so" is misleading and false without evidence.
I'm no apologist for the company. It did a number of nasty and racist things, but it also set up the first clinics and schools in the areas where it operated and brought relatively high paying jobs in places where people barely got by on subsistence farming. The history of this company belies any easy categorization or moral judgments.