As was said, the tunnel is so deep its more than likely below the storm drains, which means a sump would be used and therefore increases the chances of something failing by ten fold.I highly doubt Alton Towers would have built the tunnel without a drainage system. I find it very hard to believe that the height of water could raise above the level of the tracks enough to stop a train traveling through. Would have to be atleast a 4ft deep puddle which would take one hell of a storm to create or a blocked drainage system for a good few weeks.
British summer rain storms are far far worse now than ever, and by far are the worst rain storms of the whole year. I have first hand seen areas with much greater surface area than the base of the Oblivion Tunnel fill with a substantial amount of water in a matter of hours. I would say if the sump was to fail its a very real possibility that the tunnel could reach a critical amount of water in a reasonable amount of time.
As for stalling, that's a different kettle of rather large orange and black fish alltogether.