>so the spanish inquisition, or the burning of witches, and whatever else atrocious people did in the name of religion was ok
Absolutely, yes, if you ask the religious people who did those things. Of course, non-religious people (or people of a different religion) disagree, but that's simply a difference of opinion.
>have you not noticed how christianity has changed over time?
It's changed in many ways, and depends on which group of Christians you're looking at. Are you looking at the Mormons, the "supply side Christians" that are popular in American mega-churches, the rather liberal Presbyterians, or what?
>is everything religious leaders and people do in the name of religion today backed by their holy scripture?
I'm pretty sure it is. You can interpret that scripture an infinite number of ways, so they always seem to find some way of supporting their claims.
>there is room for improvement.
"improvement" is your opinion only. For them, your idea of "needed changes" are anathema.
>this is exactly what jesus did,
Jesus specifically said (if you believe the quotes in the bible are true) that he did NOT come to replace anything. Of course, the teachings attributed to him are quite different from the religion he claimed not to be replacing. And of course, there's no real evidence to support any of this, either his existence, the words claimed to have been said by him, the previous religion the people in that region followed, etc.