The slide over view should only come up if you swipe from the very edge of the screen, and centered from top to bottom. If you swipe up or down from the center you just get a little tab you can use to pull the panel out.
If Flip Board has a slide from the edge gesture, then avoiding the center might work. If it is just a swipe right to left on the left side of the screen, then avoid the very edge of the screen, and slide over should not activate.
Worst case, if you have absolutely no use for slide over, it can be disabled under Settings > General > Multitasking.
Since Apple has co-opted pretty much all the swipe from the edge directions at this time, I expect most apps that use that gesture will be updating to another method soonish.