No. I've charged mine in the iPad dock with the Smart Cover still on. The Smart Cover covers the front of the iPad, so it won't get in the way between the male end on the dock and the back end of the dock.
I kinda tried to do it but it seemed like a tight fit so I was afraid I might hurt it and your answer really solved my question but I am new here and I messed up and only selected that it helped me. Sorry for that. Thank you very much!