If the problem is that people seeing the comic through such client do not see the banners, then
why not embed the banners in the comic image?
I mean, instead of serving the banner as a seperate image, buddnle them.

Like:
[@][@][@] <- panels
[=======] <- banner

How about this? You can even randomly flip the top and bottom banner/panel arrangement, as to prevent thick clients from using image cropping to leave the banner out).