I'm not sure what you mean by isometric angles not being linear. If 0 degrees is to the right and 90 degrees is down then with 1:2 isometric the vertical speed should half the speed of going horizontal. sin and cos aren't a reason for why it wouldn't work.
Would it be simpler if you just did all the motion as if in top view and convert to iso by dividing all y positions by two?
isometric game basic based on "Pathfinding demo"
Can you integrate isometric rules for playercontrol (Rotation/Speed), please? Is it possible that the enemycontrol is limited to 24 way?