I don't actually see a problem with this. Unless you think there would be a problem with a news station refusing to run an ad stating "Hillary Clinton attends Nazi rallies!"
First, you need to separate the ad department from the editorial/news department.
Then you need to assume the ad department had enough of a concern about the accuracy of the claims to worry whether they would have liability if they ran an ad they knew to be false (probably very little because its about someone political, though not an elected official).
If I recall, the NYT and many papers refuse to run anti-abortion ads. I don't think this is problematic either. Ads are ads, and decisions about which ads to run should be subjected to different criteria than decisions about which stories to run.