I think the best way is to manually allocate citizens in your city to work for things that generate more gold / production / food / culture over science.
For example, if you leave your citizen allocation for the "governor" (the AI), it will surely prefer a "2 production / 5 science" hex to a "2 production / 1 gold" hex, even though the latter is better for you. Remember that for manual allocation you must first open the citizen allocation menu in the city screen, and also remember you can allocate citizens in buildings, for the buildings that allow it (called specialists).
You can also leave the allocation to the AI and only direct his effort by choosing something to focus on, via the radio buttons in the manual allocation menu. Those work better when you want something specific, though, not when you want to avoid something specific.
Finally, remember that even after you have researched everything, you can continually research the repeatable "future tech" technology for extra points. It gets harder and harder to complete it every time you repeat it, so you can never have too much science if you go this route.
By the way, if you have built any academies you can now override the hex containing them with some other improvement / great person structure, that can also help if you want to redirect your efforts elsewhere.
EDIT the newest version of civ5 allows you to sell buildings - which is perfect for this case! Just sell all your research labs, universities, libraries etc. - sell all buildings that only give you science. Since you can sell only one building per city per turn, I recommend you start by selling the buildings with the highest maintenance cost.
"Simultaneous" in this context doesn't mean everything happens at the same time, it means every player takes their turn at the same time (not sure about the AIs...), pretty much with the rules you'd expect in single player - if you tell a scout to move, it will move straight away.
So, in your scout sceanrio two things could happen:
You move first: Your scout moves away, the archers cannot fire because they are out of range. The archers are still free to move as usual.
They move first: The archers bombard your scout. Afterwards you can still move your scout (assuming it is still alive).
I've not played a lot of multiplayer, and haven't had a really intensive war yet, but I imagine there's a little bit of "fastest trigger gets an advantage" in situations...
Best Answer
You can finish your turn with Shift+Enter at any time.
I didn't observe what happens if 2 units "illegally" stacked (I.e. building a unit in a garrisoned city).