Crazy. Expensive. But very doable.
It can be done if you are willing to shell out the cash and be completely exhausted on Sunday.
What you'd do is take one of the first JR Tokaido Shinkansen trains from Kyoto Station to Tokyo Station. It's a 2~3 hour trip to Tokyo depending on whether you're on the special rapid or not and costs around Y12,000 one way I think. From Tokyo station take the JR Yamanote Line to Osaki Station. Then transfer to the Rinkai Line going towards Shinkiba. Get off at Kokusai-Tenjijo and follow the herd of people.
If you leave Kyoto at 6:00am or 7:00am you should probably get to Comiket around 10:00am~11:00am. That'd get you a full day as if you were already in Tokyo. After it's over just reverse steps and you'll probably get back to Kyoto 9:00pm~
It'll run you a good Y30,000 to pull it off, but it's actually very doable. I got called into work in Aomori while at Comiket once... So I've done the Tokyo Big Site to Shinkansen run before.