How can you avoid this issue? Well, you could just go to the International Space Station and do your astrophotography from up there.
This is only possible for a very select few, but astronauts Andre Kuipers and Don Pettit captured some orbital views of the Venus transit on Tuesday to give us a taste of the historic event through a lens not hindered by Earth's atmosphere.
Kuipers, who posted an impressive photo of the transit (above) to his Flickr page, said, "With our orbit along the border between night and day at the moment, we could often see the Venus transit for long periods of time."
Whereas many places on Earth were frustrated with bad weather or not being able to see the 7-hour transit as most of it happened during the night in their location, the space station experiences 15 or 16 sunsets and sunrises every day, so it avoids these very terrestrial problems.
During the Astronomers Without Borders (AWB) live Venus transit event atop Mt. Wilson, Calif., I had the great fortune to be surrounded by an army of astronomers with some of the finest telescopes on the planet. Using my camera, I was able photograph the image below (right) through an eyepiece as the sun was approaching the horizon at the end of the day. As sunlight travels through more atmosphere when the sun is low on the horizon, a lot of atmospheric turbulence is evident - giving an otherwise smooth solar limb (and Venus silhouette) a wobbly appearance.
Compare that photo with Kuiper's shot (left) - this is what the transit looked like without a meddling atmosphere in the way.