My current theory for if you choose to max out your Illithid powers is that you could end up turning into an Elder Brain. From what we see in the beginning of the game it looks like the Mindflayers on the ship are in a rush to reproduce and even have tech on board to speed up the process. Maybe they just needed more crew to man the ship or maybe the Githyanki attacks have pushed far enough into the Mindflayers' territory as to endanger the Elder Brain commanding them.
It would make sense then if the Guardian is actually the Elder Brain coaxing you along the path needed to become its successor. It wouldn't really be lying then for it to say it's protecting you as maybe in order for someone to skip along the Illithid lifecycle - from tadpole directly to Elder Brain - they first need to cultivate a great deal of psionic ability.
At the very least I think this would be pretty neat!
