This was a bug in two places - broken even before 1.0, and cutscene in 1.0 added another minor incompatibility.
Fixed both in 0.3.2, should work as expected, I think, but do let me know if it still does not.
Btw, there's quick way to check wisp-player aggression settings via console ("tilde" key on the left of "1"), using "/wisp stats" command there.
It should print like like this: "wisps: cease-fire-settings w/p=peace/peace wa/p=war/war w/b=peace/peace wa/b=peace/peace"
There, "wa/p" is always "war/war" (that's relations of "wisp-attack" vs player force(s) - always war), but w/p is the one of regular wisps vs player(s), and should depend on settings (e.g. player can be aggressive to wisps if "turrets shoot wisps" option is enabled). "w/b" and "wa/b" are relations against biters.
Pre-0.3.2, w/p always showed war/war, due to those aforementioned bugs.
0.3.2 should run migration to fix that when installed, and not have this issue in new games.