Towards the bottom of the descr_strat file, there are values for diplomatic standings between factions. By slightly altering a few of these I have been able to get a (slightly) more reasonable diplomatic AI.

Although I've only tested this for about 50 turns, the HRE and Milan (I'm playing France) don't seem to want to kill me straight off the bat, and although they do still attack, they seem a little more reasonable in negotiations.

I imagine this will be possible to tune even more once the unpacker is released and we get to have a look at all the other files.