I haven't read the manga. In Code Geass R2, Lelouch orders Guilford to think that Lelouch is Cornelia upon taking a specific pose. It would seem like he did this just as a precaution before meeting with Suzaku.
But, why not just order him to protect Lelouch when he takes such pose? What particular advantage is there on making him think Lelouch is Cornelia?
There is no manga that I know of that would be more canon than the anime. So do not worry about "not having read the manga".
The advantage of having Gilford mistake Lelouch for Cornelia is that he can leverage Gilford's loyalty to continue giving him orders as long as the Geass is under effect, and having Gilford take whatever initiative necessary that is advantageous to him.
For example, after Gilford had vanquished the guards, he was able to have Gilford take him to a location of his choosing. A simple order to "protect him" would probably have made him a standing duck, as the Geass would have lapsed or stopped driving Gilford to action, as soon as Lelouch was "safe".
That ties in with my opinion that the practical reason for Lelouch not to give blanket orders for people to obey him (as he began doing after some point) was that doing so basically reduces people into living robots without initiative or self-preservation.
