Well, there was a reason. Whenever you add a sprite from disk - either dropping it on the IDE or loading via the file requester, I didn't want to have a dialog pop up to ask about whether you happened to want a colour removed. This I believe isn't the norm. Alpha is now prevalent through 2D, both in basic transparency (on/off pixels) and to allow smooth anti-aliasing of sprite edges. Because of this, it means removing a colour is very much "the old way" of doing things, and as such for an IDE that's looking forward, not something I wanted as the default way of doing things.
I don't mind having extra tools in the image editor to allow you to do this, but I certainly don't want the default import to have it. For importing of animations, (which already has a dialog) we will look to add it into there it won't hurt or interfere with the process.
You may not agree with these choices, but these are the decisions we've made.