should i try and teach her the "right" way to shoot?
Yes, if and only if there is no compelling reason for her to use her middle finger to pull the trigger. In general one should simply do whatever works the best, regarding everything--don't let others who are different dictate to you the "right" way to do things just because their way works the best for them (if even that). On the other hand, when there is no valid personal reason to do things differently from the norm--especially when equipment is expressly designed to be operated a certain manner--then one should train to do things normally to help avoid problems.
If your wife can shoot just as well with her index finger (with some practice to get accustomed to it), then she should do that because it helps avoid certain problems that have already been mentioned, such as being injured when shooting a revolver. When shooting handguns of any type, using the index finger also allows for a firmer grip, which is always a good thing.
Otherwise, if she has some physical issues to overcome, then have her do whatever works the best for her. For example, I've heard about people who use the index fingers of both hands to shoot double-action revolvers--maybe this is not ideal, but if it is demonstrably the best method for them, due to limited strength, then I for one would not tell them that they're wrong. I have even suggested that certain people consider single-action revolvers (like the Ruger Vaquero) and learning to "slip-shoot" with their support-hand thumb.
Is this as ridiculous as it may seem at first glance? Well, for those who can neither rack a slide nor pull a double-action trigger reliably, perhaps not--whatever works the best for you.