Imo "horror" ceases to be horrifying when the thing hunting you can be dealt with easily.
That's why games like Amnesia the dark descent is scary and the shootem up and nuke the monster games aren't as much imo.
I can see balancing this in a few ways:
* Have the hunter show up later in the game on his own ship that docks with the Nemesis, giving less time to complete the objectives.
* Potential to also need to fight against the crew members, reverse their efforts, make sure the ship doesn't reach Earth etc.
* Need to defend his ship against intruders and crew members attempting to escape while also working to complete his objective.
* Have "unplanned" abilities of the intruders that the hunter isn't aware of, making much of his prep work worthless (he brought energy weapons, suddenly they adapt and can no longer be damaged by or take reduced damage from energy weapons).