What's the bottom of the pannier made of? Just fabric? Some have thick, waterproof bottoms that would be hard to fix by sawing. Sawing a nice, large patch is probably a good idea. An iron patch would likely not be strong strong enough, so I'd still reinforce it with some stitches. A tent repair patch maybe? But, still not strong enough. I'd probably go with sawing, although you may glue to patch first with a fabric adhesive.