Hmmm... Well, I'm not going to categorically say it's fine, but the -12V isn't critical to the workings of your Amiga - in fact, it'll still work fine with it totally disconnected apart from sound and serial. My guess is that it would be fine - I've measured the -12V on PC power supplies and found a number that are a couple of volts out, yet the machine works fine.
Another issue may be that if the -12V isn't regulated (and I suspect it's not), measuring it while it's not connected to the machine may give an increased voltage (well, potential difference) due to the lack of load.
OTOH, an Amiga motherboard is far more precious than an old PC motherboard, so if you don't feel comfortable trying after what I've said, wait for someone else to come on and say it's ok :-)
