Surely if they can TRANSPORT the mobile emitter, break the bastard down into energy, hold it's pattern during transit and then put it back together again, then they can REPLICATE it... Since the Replicator, holodeck and transporter are all from the same family of technology.
I like the idea that Janeway just didn't want to replicate the emitter because it was sort of immoral to keep the emitter and TOO immoral to massproduce it since that would make her just like Starling.
besides if the Earth hadn't already been destroyed in the 29th century then it's fortunate that the mobile emitters presence in the past created an alternate 29th century, not that Janeway wasn't expecting some one to turn up sooner or later form the alternate 29th century or an alternate alternate 29th century claiming that she was polluting the time line with disingenuous technology.