I agree with Dias on that - I can’t see the Advisors making you hallucinate beyond messing with your vision as we’ve seen before. The Combine is ruthlessly efficient - they’ve been pretty clear they intend to destroy Freeman completely, not mess with his head for the lulz. Also, I think their motives are have been fairly clear:
A. Main Objective - Invade planet Earth, destroy all sentient life and take its resources.
B. Secondary Objective - After Breen convinced them that we would be useful, experiment with humans as a new combat force, utilise human technology, and test them on the rest of the human populace, while continuing to drain Earth’s resources. Since the humans aren’t much of a threat at this point, return most of the invasion force off-world leaving a small, mostly transhuman garrison.
C. Freeman wreaking havoc and citzens revolting showed the transhuman forces aren’t really worth the effort and resources, despite Breen’s protests, so they revert to the Main Objective.
D. Need to bring back reinforcements, but Citadel and other interdimensional transports are out without any easy way to repair them. Make Citadel self-destruct allowing the opening of a super-portal.
E. Gordon and Alyx infiltrate the Citadel and acquire codes that can close the super-portal before reinforcements can be transported through. This potentially jeopardises the whole operation. Reclaim the codes and destroy them both Also destroy White Forest as it has the rocket that can be used to transmit the codes.
F. Acquire the Aperture Science technology in the Arctic. This is the most unclear motive as we don’t know what it is yet, but it’s presumably some kind of interdimensional teleport that could be a backup for the super-portal plan. Now that the super-portal is closed, this is their only way of getting reinforcements and returning to the Main Objective.
The only thing that doesn’t seem to immediately follow from these motives is breaking in and attacking Eli. Perhaps their main targets were Gordon and Alyx and they just picked up Eli first, perhaps Eli had knowledge they could use and they drained it out of him, or perhaps they were manipulated by the G-Man somehow. In any case, they have little reason to make Gordon hallucinate - they want him dead and out of the picture as soon as possible, and will do so whenever they have the opportunity. Messing with his head seems a lot more like the G-Man’s style. God, I wrote way too much, I hope it was somewhat interesting to read.