Getting nasty with the gate agents won't help you, even if it's an airline screw up. I've learned that the hard way myself, and now am really nice to gate agents, and if they say no, I realize that arguing won't do me any good.
I would have been super nice and asked to wait til the end of the boarding process to see if any better seats would open up. Then you may have been pleasantly surprised.
I suspect what AF did is cancelled your seat assignments so someone else could sit together. ANd since you both were on separate PNRs, they probably didn't know to keep you together.
IMHO, it's wrong to change someone's seat assignments at all, especially after check-in, without specifically checking with the pax first, but realize that AF was just trying to accommodate another customer.