Did you put it, in your discussion with them today, the way you did for us in your post? Because, with a few tweaks, you put it very well:
"There is nothing in my report that wasn't discussed with you in person during my visit."
"You've said that everything in the report is fair and accurate but your concern as I hear it is that you are worried you will be blamed for these things. Am I hearing that right? You are not being blamed for things that were going on before you took over. I realize you just recently took the lead there. But you do now have the responsibility to fix them. This report is intended to help you do that, not to blame you."
"Your next corporate level audit is due in a year or so. This report can help you address issues BEFORE that audit takes place, so that you can have a good audit when it does happen. It is much better for your division to hear this now, from me, than to hear it for the first time in a corporate audit where everything is on the division's permanent record, so to speak. I am available to answer questions and to help you well before corporate comes in and gives its assessment."
And visit them again soon - don't let the fact they're pissed make you find reasons to stay away. In fact let it make you go there much, much sooner. They will of course think "She's checking up on us!"
Well, you ARE. That is your job. Do it without apology. But yes, do it while building the best possible rapport with them. Tell them that in so many words - "I want to build rapport with you and this report is intended as a frank outline of what can be improved and aren't all of us interested in improvement?" Then get them the resources they need to make changes happen. If you had issues with certain things do they actually feel (though they may be scared to tell you this) that they don't have the money or people or corporate support to make changes happen? Something to consider.
Can you set up regularly scheduled videoconferences with all your divisions? Maybe you do that already. It sounds like this new guy is running scared; did he possibly come from the ranks and hasn't had much management training? I'd try to work with him, get him resources, let him see you are all about helping them, but do not backpedal on your specific findings or apologize for producing a report that your own boss expected from you.