I have a JB junior as the bridge pickup on my fender jaguar. It's got a great tone to it. I think it might cause problems as a middle pickup when coupled with a humbucker. Especially if your using the jem switching setup where the bridge and neck pickups are split when they're combined with the middle pickup. My only concern is having a lot of signal cancellation. You could always set it so it's split when combined with the other humbuckers. I bet it would sound pretty cool in middle position. I've always toyed with the idea of have a tricked out strat with a little 59 in the bridge, a JB jr in the middle and a mini screamin demon in the bridge! Pickups are finicky things and you really don't know what you're gonna get till you put it in.
I wouldn't do it if you want "standard" sounds, because it won't compete with a real single coil when you split it. But if you want something non-standard, say, a middle position bucker alone or in combo with another pickup - go ahead.