You either use StrokeIt or Opera's built in gestures, you can't have both at the same time. So if you want to use StrokeIt to switch task while browsing in Opera you'll have to enable it there. Doing so you'll lose Opera's built in gestures and you'll have to re-create them in StrokeIt.
An alternative is to use the disable key (ctrl by default) to make Opera's gestures. But the point of task switching (and anything else) with StrokeIt is not to have to use the keyboard at.
By the way, I still think that the taskbar is just as good for that purpose and alt-tab on the keyboard is even faster.