It is true that sometimes we have to make our pets uncomfortable for a few moments for their own good. I've had lots of Persians over the years, so trust me, I know. In your case, removing the matting in your cat's coat has certainly saved her from skin diseases since knots prevent the skin from breathing and can result in nasty skin infections. You did the right thing.
To avoid hair clumps, common in Maine Coons, you should brush your cat everyday. It is possible to educate animals to accept daily care (clipping, brushing, taking medication). And, as a matter of fact, giving tuna to your cat was the right thing to do: to associate the treatment with a reward.
Take advantage of moments when you are stroking your cat to brush her at the same time. At first the brushing sessions will be very short, but if you increase the brushing sessions with treats, the cat will combine the two and put up less and less resistance.
If it's too hard to do it by yourself, don't hesitate to bring your cat to the vet. It's hard being a pet parent, but hang in there! :)