I don't think this is possible.
- first (and most importantly), if the iframe is in a different domain, you can't change its DOM - such as the onunload handlers. If this is the case, the other two issues are moot.
- second, even if you could, you'd have to remove the listener in some way. If the listener is loaded via window.onunload, that would be simple; otherwise, not so much.
- third, in the long term this would lead to the same arms race as the frame-busting-busters
The only possibility I see is non-technical in nature: check with whoever runs that site inside the iframe if they could make a special page for you, one without such onunload popup. In most cases, either
- a) some special arrangement can be made (although not always for free), or
- b) removing the functionality would be a violation of the ToS, in which case you'd have to look for someone else providing similar functionality, without the pop-ups (and realistically, most services have more than a single provider)