I am running a campaign with PC characters from EotE, AoR, and F&D. I have an inquisitor as the main BBG through the story. However, I don't want him showing up every game session and diminishing his stature as a BBG. I was going to introduce an Emperor's Hand as another Force sensitive Imperial to challenge my PCs. I have not found any EU references to either parties working together or references to indicate if the Emperor would allow these two factions to work towards the same goals for him. The Hand's mission goals will not necessarily line up with the aim of the inquisitor all the time.

My PC unknowingly revealed their Force abilities and lightsabers in front of the inquisitor while attempting to rescue captive Jedi survivors from the Imperial prison on Dathomir. Needless to say the intel that led them to these actions was false and planted in the ISB databanks by the Inquisitorius to root out any remaining Jedi or Force users intent on finding Jedi. Any feed back and suggestions would be appreciated.

Are you wanting a second Force sensitive adversary? or a second imperial adversary who is Force Sensitive?

If you just want a second FS adverary, what about a 3rd faction? Maybe a rogue/corrupt/insane Jedi that has set themselves against the PCs for nefarious reasons? The PC could have been a padawan when his Jedi training had ended and now he/she does other things.

I want an Imperial advesary who is Force Sensative and is directed by the Emperor. My main theme would be to demonstrate that the Emperor will work all the angles and pit his minions against each other as long as the overarching result is to achieve what he desires. I want to force the Hand and the Inquisitor to face off at some point.

It's Palpatine - he loves pitting people against one another and entrenching them in his machinations. Your adversaries don't need to cooperate. In fact, having them at each other's throats/constantly trying to outpace or outmaneuver one another in pursuit of the players, is probably the most fun outcome.