Dr. Breen was the Administrator of the Black Mesa facility in Half-Life, and there is mention that he was the one who obtained the crystal that was instrumental in the opening of the portal. There were dead survey teams on Xen, where the crystal originated, and there is also suggestion that the G-Man obtained a sample, but it is unclear from which avenue the test sample came into the Administrator's possession.
This all suggests that Breen was fully aware of the origin of the crystal, and possibly what effect it would have. He could, essentially, have been working with the Combine all along, and orchestrated the events at Black Mesa that led up to the incident, because he refused to listen to the concerns of the other scientists there. He could have made a deal in which he would become the 'Adminstrator' of Earth in the ensuing aftermath of the seven hour war, and then (like all dictators) manipulated events to make it seem that he had saved humanity.
Gordon Freeman, by contrast, was essentially used as a pawn by Breen to open the portal, then later manipulated by the G-Man who seemed to be working against the goals of the Combine. Should Freeman have stopped and questioned why the experiment was to go ahead when so many things seemed to be going wrong beforehand? Possibly. However, it is debatable what that would have accomplished - he could simply have been replaced by another scientist to carry out delivery of the test material. The outcome would have been the same.
Had Breen actually been working for the benefit of his fellow humans, he would surely have attempted to find ways to scupper the end goals of the Combine in the longer term, yet there is no evidence of that - in fact, the complete opposite happens as he willingly complies with everything the Combine wants, with the apparent eventual goal of becoming one of them. Even when it becomes clear that the resistance is working, Breen seeks only to save his own skin and join the Combine, so his personal motivation is quite clear.
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