This must be a special new meaning of the word "non-intrusive" that I wasn't previously aware of.
Of course it's intrusive, otherwise it wouldn't be effective advertising. It's designed to interrupt the reader and distract their attention away from what they're doing to the ad. It's the very definition of intrusive.
What's particularly destructive about pop-up ads (as opposed to the banners we've all come to accept and ignore) is that it obscures the text. Since the text is the value of the site, it effectively devalues the site.
If I'm reading a thread for specific advice or something I'm intensely interested in, I'll put up with the annoyance. But if I'm casually reading a moderately interesting thread and shit starts popping up I'm gone. I suspect most readers behave similarly.
So I predict that this will probably not scare many people completely off letsrun, but the overall traffic will subside and it will leave you more vulnerable to competition from more user-friendly sites.
Do what you think is best, but this ain't "free money."