Fajo made it clear that in Data's present circumstances, Fajo's continued existence presents a certain threat to the well-being not just of Data but of others, too.
Treating the show just as a drama, I can buy that, though looking at it more as a real world situation it seems to me that Data could probably incapacitate Fajo and take control of the vessel.
How would Data have been able to do that? Data couldn't get close to Fajo because of the proximity-actuated field.
He already tried numerous other forms of resistance throughout the episode, and this was his only chance to get ahold of the disrupter.