I do it by sanding back the heavier blade, and have never had any structural issues. As for altering the section, it won't be any worse than painting the light blade!

When it is balanced, however you do it, try turning it through 90 degrees about the length of the prop. If it then appears to be slightly out of balance it is due to the hub being out of balance. The side of the hub that is uppermost when it is out of balance is the one that is heavy so sand that side back. You might be surprised how much out of balance the hub is. Again, I have never had any issues with prop strength by removing material like this.

Also, if possible, try balancing the spinner. Most will be out of balance by at least as much as the prop was, it can be balanced byt drilling small holes as necessary in the backplate.