In the first scenario once the final railroad faction has been shot and the courser is moving toward the railroad, is there anyway to slow his progress? Once he reaches the railroad the institute gets moved forward five times which makes someone win the game.

Can this be stopped?

No. The Courser cannot be stopped. The only hope the railroad has at this point is to spawn enough Railroad tokens that the Star Faction maker moves down the track and they win the game before the Courser get's to the Railroad HQ.

...and that requires a TRUCKLOAD of money. It's not a fun spot to be in.