Answer by Ashley
As alpha layering is supported and that pixel manipulation might be unhandy in JS, color to transparency probably won't be a feature of C2.
Also in GIMP, take your spritesheet, use the tool "select color" set it's tolerance to 0 and select the background color. Be sure that your layer has an alpha channel and delete the selection. This should do the trick for your whole spritesheet.
A little search would have given you the answer.
I also edited the title of the topic.