The workaround has been like this all the time. You need transparent pixels around the objects. otherwise the filtering will use pixels from other objects..
For sprites this is easy to fix on your own, and should be standard for all imported graphics already. Also for graphics you create on your own within the engine.
The problem as I see it, is if you have lot of background images, which cannot use transparent corners, since they should be tiled..
Maybe the engine should add some transparent pixels between all objects when creating the sheet automatically, enough to cater for all kind of filtering combinations. But this would need a code fix for the engine and editor. Don't know how hard it would be to do