Can I even out an entire ocean with world edit?
There are two steps here:
Having decided on the level you want your sea to be at, first make a selection of everything below that level. Be careful though - too deep and you'll fill caves! Just for aesthetics, selecting just the surface blocks will be fine. Once you've made your selection, replace air blocks with water. You may need several selections to get the fidelity required.
Select everything above your sea level and replace water blocks with air. This is less dangerous than the previous command, so you can be generous with your selection.
When you reload your world, your ocean should be back to being smooth and flat!