Yes, it should be possible. All you need is a WHDLoad installer which installs your CD32 game to AmiKit. More info here: http://forum.amiga.sk/index.php?action=vthread&forum=2&topic=1464
Another possibility is to bypass AmiKit completely and alter the WinUAE configuration as explained here:http://wiki.abime.net/emulation/winuae/cd32
Once you create a custom configration, save it under different name, eg. CD32 config. From now on, you can simply run AmiKit launcher, press Configure WinUAE, load your CD32 config, mount your game into virtual drive and play.