"Don't need empathy to know he's pissed," Eliot muttered as he looked after Dean trying to strangle the life out of a plate, that was before trying to drown it and torture it with the rag. After watching Dean for a while, Eliot got the good sense to leave him alone and addressed Sam directly instead.

"Still... too dangerous. Ain't there a way to stop this telepathy or empathy thing without breakin' the bond?"

Because Eliot wasn't trying to get rid of Dean, he was trying to eliminate all these strings attached that would potentially get them killed. He didn't know how dangerous was what Sam and Dean did for a living, but hunting monsters couldn't be that simple a thing either.