So given that, how would you strand them?
Well, I'm glad you asked!
I would have spent most of the pilot episode (or possibly several episodes) at home with these characters. Get a real sense of their relationships with folks at home or in their current roles, their problems, their flaws. That way we care about them and we truly feel their pain when they do end up getting stranded away from home. I would have had a flashback scene with Paris and Chakotay, for example. I would have had Tuvok get caught by the Maquis and held hostage by them (more tension for later). I would have had Janeway in an actual scene with her mate. I would have had a scene with Harry Kim and his proud mother. Like I said, I would have had that first officer guy be the actual captain and have some great scenes with him too so there is an emotional impact when his is killed. Things like that. Then getting to the Delta quadrant would have been a quick matter of perhaps the tri-cobalt device firing inside the briar patch causing a temporary "man-made" wormhole, sending them on a one-way trip to the Delta Quadrant. The unique elements of the briar patch combined with the tri-cobalt device somehow caused the wormhole, and it sent them at random to the delta quadrant, then collapsed. So even if they could find a similar briar patch along the way, there is no guarantee of where it would send them if they were lucky enough to recreate one of these wormholes. That's just off the top of my head, but the point is, get them over there with no immediate solution available, that way Janeway doesn't look like a fool for destroying their only immediate chance of getting back. Oh, I'd also have a Cardassian ship become stranded with them, and the Cardassians end up on board Voyager as well. Tension, baby!
Since this is way too much to fit into a 2 hour premier, I am going to assume that you mean "story arcs" that span more than one episode. (and please feel free to correct me.) Now you just hit on the second problem. Voyager was a network show, the same as TOS which introduces a second layer of executive oversight, the same second layer that Enterprise had. And per UPN, said network, there was to be no story arcs, and that directive was in place from the beginning of Voyager through the first three seasons of Enterprise.
And Melakon, I agree totally, I can see the POV that destroying the Array was not only within the scope of the Prime Directive, the directive required that she destroy it.