Short answer: No.
Longer answer: Whenever you spawn a new window in IWP, it creates a "virtual" window in the browser. The window doesn't really overwrite the original window; it's still there (you can demonstrate this by using a Close Window script step using the name of the newly-spawned window), but it does "take over" the browser space, as you've observed.
Would you be willing to indulge my curiosity as to:
1) The nature of what the new popup window would accomplish?
2) Forseeable plans for moving out of IWP and into WebDirect?