I have used plain peroxide on scratches like yours, just pour it on, repeat until it stops bubbling, it does not hurt and you end up with hardly any scars, but do it right away, the longer you wait the more you will scar. I've done it with bites too and got no infection and no scars. I don't take care of ferals but foster and those can be pretty traumatized by the time they come to me, they've usually had several fosters before I get them, somebody seems to think that I have the magic touch so I get these "incorrigibiles" after nobody else could get them to be "normal" cats. One I have now had for 9 months, he's better but still not adoptable because of his behavior.
Just noticed this thread now.
Wow, you've done a wonderful job of taking care of those cats! You were really successful with the trapping, it took me months to get the colony I care for all fixed and I actually gave up on a few of the Houdini male cats because they were too smart for me.
I've had some bad scratches too. I don't think they're as bad as bites, which always seem to get infected, but make sure you clean them up, put plenty of antiseptic on them and keep them covered until they scab over.
Beautiful, beautiful cats and kittens. I think you should apply for our Friend of Feral badge, your deserve it.
http://www.thecatsite.com/t/251561/friend-of-ferals-award-badge-apply-here