Re: Bida'a...
i can tell you where your reasoning is wrong, i cant change what you will think though.
one could extend your argument about the unimportance of niyat to saying that Muslims worship a stone (Kaaba) and run between mountains thinking that will bring them good. That is often an argument Hindus make to justify idolatory, and the only answer to that is that the Niyat of Muslims is to perform those actions for Allah, and those actions do not have any inherent significance except for that granted by the single Allah and his last Prophet. These actions do not invalidate those beliefs. Thereby you too perform actions for which there is no inherent justification against justifiable allegations of "stone worship" except niyat. from the outside, anyone seeing thousands of Muslims milling around a stone and throwing pebbles at three stones as stone worship.
First off you cannot compare rape and grave "worship" as that is a crime against another human being. Secondly it is very hard to offer plausible alternative niyats for a crime like rape. If however, there is an action that is not a legislable crime against another person and that does have plausible alternate intentions, I would have to take the other person's stated intentions as the truth when casting judgements of Kufr about his beliefs. You cannot call people liars to their face, and then call them Kaffir, because here you're going on a limb guessing what their beliefs are, and IF you are wrong, you are wrong on an extremely, extremely serious thing, and according to Hadees, risk being a Kafir yourself.