It does sound like youve gone about it the "wrong way" in that I mean not the genereal accepted pipline for rigging and then animation.

Whai I would suggest to do it to detach the skin, then select the joints (or control object if you've used them) that youve moved and in the channel box select the keyed attributes, translate, rotate etc (or all of them if you set a key for the lot) right click and then go to break connections, the pboblem then might be if youve added any controls or constriants they might be broken too, this should get rid of the animation.

Like R@nsid said, if youve not painted weights yet you shouldnt have to go back too much. also save a copy before doing this incase it all goes wrong.