In an effort to get back to the original matter at hand…
The Yonkou don't even count as a group anyway, due to each being a rival to the other three. While the Shichibukai aren't allied, they don't seem to be openly fighting each other.
And the Navy Marines, well, I still say they outnumber both groups combined…they'd have to for the world to maintain balance between the law and the outlaws.
So, my theory is that the Yonkou, if they ever allied, would be a threat the Navy Marines couldn't safely combat without weakening their positions elsewhere, unless they could rely on the aid of the Shichibukai.
Individually, though? Each Yonkou is not some godlike power that could take down the entire World Government, they're just really scary pirates with many followers.