Exactly. Minimize the risk to the civilian population as much as possible.
The saucer was "infected" before they knew anything more. Remember the door to Picard's Ready Room didn't open, until his second approach? So the virus had spread into different systems around the ship already.
I think the point here was more to get the bulk of the crew away from the warp core. No doubt other things could kill the crew (life support comes to mind). But at least the risk of a warp core breach was removed.
Were the Neutral Zone Outposts ever rebuilt? Seems you could have parked the saucer near one.