Lol that ain't possible.
Cerberus will always stay your enemy.
Ending spoiler!
You will kill the illusive man in the end of the game. That's how it will always go.
No, as Nick said, that will happen every time, and they are always your enemy.
Also, I know what your problem is, persuasion options are unlocked depending on how much paragon/renegade you got. If the "We should work together" one which I highly believe is the top left one, is grayed out, then you do not have enough paragon to use it, but if the bottom left which is your renegade option is actually red, then you have enough renegade to use it. I also assume you built an evil, bad character, aka renegade. If you do the good options during your next character, you will most likely have it unlocked on your next playthrough.
If you don't know, top right = Paragon, middle right = Neutral and bottom right = Renegade options in chat, always.
i made evil character
i have only renegade points no paragon at all
it worked to me on some mission
on the mission at the citadel when kaiden wanted to shot me i had both persuasion opitions unlocked even when i was evil
btw:can i ask what happen if i use them while talking to the iillusive man for the first time it appears??