Yes, mission control is a completely abomination on multiple monitors... I use a 4 screen setup, 1 of them is a 140 projector for movies... so i definitely understand what you mean about the movie issue.... MC isvery very limited in what could potential be a step up from Spaces... instead is a step backword...
1. no way to lock monitors (such as you are talking about with watching a movie)
2. no way to move windows from one desktop to another... Spaces was great for organization... MC is a very dumbed down version.
3. Spaces showed all "desktops montitor groups together" where the way MC splits them seems unnatural and odd to me... makes sense on single monitor, but horrible on multi monitors
4. Full screen apps are worthless with multiple monitors... it should give me the option to do full screen app on EACH monitor... this would definitely ogranization.
Way late, but if you right click on the app, go to options and then Assign to: Choose All Desktops. This should keep your movie on the second monitor. The caveat though is if you are watching netflix through safari and open another window, this setting will also bring the other window with it. so a partial workaround I guess.