If you don't want IWT spammed you can either control it through a modifier action or you can step stagger so it only attempts to IWT half the time.
To totally avoid the IWT runaway issue I just did something similar to what Fat Tire is talking about. One key to IWT, another to stop and disengage IWT for a second or two. I also had UI toggle buttons to turn off IWT on specific roles. Like tank, melee, range, all, etc.
Another neat trick is to have your melee follow your ranged like a hunter. This way the hunter will always be within about 40 yards of your melee. So if the melee lose target you hit follow, the melee follow the hunter and the hunter follows you.
For my setup I left the IWT separate as well.
Key  is my aoe rotation
 is my single target rotation
 is my Melee only ATG IWT hotkey