Choosing at start of the map with the ability to skip any cinematic sounds like the way to go.
Let me give you an example ; in WoW Cataclysm's final raid, the Hour of Twilight (not sure of the name), the 3 finals bosses each have a cinematic to introduce the fight, as well as an epilogue cinematic once you kick Deathwing's butt.
The first, second and third times you try that raid out, you're like "Wow, cinematics, how nice and refreshing ! And they look so great ! So much more fun than reading text !" but after that, you just want the boss battle to start.
Also, I haven't played your map, but if it's multiplayer, it sounds like some players could fall behind while watching cinematics, while others would get bored very quickly.
So once again, I'd go for optional and skipable cinematics.