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I'm not positive if this is a solution, but my guess would be that you could make a copy of the page with the pop-up taken out for an AdWords landing page, while leaving the traditional (pop-up included) page in your site framework. As far as I know, you can't have pop-ups at all on AdWords landing pages.
My current popup windows are causing Google to suspend my Adwords ads.
Good for Google!
At least Google is doing one thing right. And if you try to get around this in any way, the result will almost certainly be that Google will tighten the restrictions. They know very well how much users HATE popups.
In any case, what's the point? Everyone I know blocks popups anyway, so the real result is that you're blocking your own ad. And the trend is only intensifying, since all the major browsers now have the ability to block popups. The obvious next step is for that feature to be enabled by default.