Freejack, there's a way to kill the werewolf and get the maximum experience possible in that area. It's kind of tough, but definitely doable, because my Ventrue was able to do it. (Of course, I had a 5 in Fortitude that I kept up the whole time, but I know this would still be possible without the Fortitude.) You said you had a 3 Fortitude, though, so make sure to keep that active!
Run into the observatory building and through a few of the rooms. There's a door in one of the rooms that leads out to the back of the building. Go out that door and run over to the building in the distance. That building controls the power to the observatory, and there is a control switch on the outside. Flip that switch and run like mad back into the observatory.
Now go into the room of the observatory that is just underneath the dome. There are some stairs and a platform at the top of the stairs that has a few computers on it and also an on/off switch. Once the power is turned on, this switch opens and closes the dome. Flip the switch on and then run outside the door that just opened onto the observatory deck.
Once the werewolf has followed you outside (and he will!) you'll want to get back inside before he does. I found it worked best if you jumped off the platform and ran around on the grass for a few seconds before climbing the stairs and running back inside. Once you run back inside, go directly back to the on/off switch that opens the dome. As the werewolf makes its way toward the doorway, flip the switch to the "off" position. The werewolf needs to be right at the doorway or starting to come through the doorway as you do this. The door will close as the werewolf continues to try to come after you, and he will be crushed in the doorway! The timer will stop as soon as the werewolf is crushed, so no matter how much "time" was left until the gondola arrived, it will be there now.
End result: dead werewolf and maximum experience! Now you can take a leisurely stroll back to the gondola and enjoy the view.
As I'm sure you have discovered, the werewolf will be hot on your tail the entire time. He will probably catch you a few times and swat some of your health away, but just keep going! You're going to have to run from him anyway, so why not do something useful while you're running?
And remember, quicksave is your friend... This is tough, but possible. Quicksave every time you've completed a step successfully, so that way you don't have to start all over again if the tears you to shreds...