There is no save editor for Beyond Divinity, but there is a more manual way to add skill points:
Hex editing - gold, experience, stat/skill points.
You can not switch genders by swapping files. Character data is stored in the data.000 file; I have replaced the entire main character data, and in theory it should be possible to figure out how to change just the gender / appearance.
There is no way in-game to undo turning a species hostile, other than reloading a previous save or waiting until the next act.
If you click and hold the left mouse button down to direct your characters, you will be much less likely to accidentally attack a friendly creature than if you repeatedly click on the ground. Also, when returning to an area already cleared, you can click on the mini-map to have your characters move somewhere.
If your non-lead character has a bow/crossbow equipped and is set to aggressive, they can take care of any hostile creatures around without you having to do much. I accidentally attacked a tibar in act 2, and letting my archer take care of them was much easier than trying to chase them down as they jumped around, and killing them gave a lot more experience than reloading a save before attacking them would have.
Isolated earthquake attacks are not much of a problem, unless you are at a lower character level or have a low resistance. I teleported into a number of hostile creatures once, with 3 or 4 earth elementals casting earthquake, and the combined effect was almost lethal.
