"How much damage does he take going through glass or wood?"
Having been foricibly assisted in leaving the premises once or twice (yes, thrown out the window...), I've found that if you shield your face with your arms, curl up your hands into fists so the palms are protected, and draw up a leg to protect the manberries, you can avoid more than minor scrapes and scratches. For a cinematic game such as 7th Sea, I'd say no damage for intentionally going through a window. It just looks cool.
"What's his defense at at the end of the leap?"
If the hero in question leaped through the window, I would say no change to Defense. Perhaps I would use the mechanism of entry to dictate the Defensive Knack until said hero's next action (e.g. if you jump through the window, use Leaping until your next action; if you swing through on a rope, Swinging, etc.). If forcibly assisted, TN 5 until you can get back on your feet.
"Who's standing over him and possibly attacking him?"
I'd rule that anyone on the landing side of the window can make a Perception check to spot incoming jackass, er, hero. Success means that the people in question can act normally; failure indicates some sort of penalty (+1 to Action Dice totals or perhaps a missed action) as they take cover from the flying glass and debris.
In short, I find the "alternate full-paned doorway" entry to be highly cinematic. Face it, it's just cool. Batman does it, Chow Yun Fat does it - it's just COOL. For a game like Millenium's End or the like (hyper-realistic and sort of anal), yeah, there should be damage. But for a game with a high level of swashbuckling goodness like 7th Sea, the player shouldn't be penalized for wanting to do something inherently cinematic (unless it crosses over from "swashbuckling" and "cinematic" to "ludicrous" and "just fookin' dumb." Heatstryke trying to leap to the chandelier chain when the stairs were right freakin' there springs to mind... Anyway, that's my take, how I would judge it in a game.
