Hi Brian - You're thinking right about taking care to make the canoe sound again. Shortcuts might easily be regrets later. On the other hand, it can be easy to obsess more than needed. Many people on these forums have been where you are, and many are working through projects right now. Just keep sharing, asking questions, and using the good advice you get.
As for punky wood, if it's really falling apart, it's best to replace. But many times things are repairable. If you don't already know about it, check out clear penetrating epoxy sealer (CPES). It's a low viscosity epoxy that really soaks into wood, deeply, especially into end grain. You just need to figure out how to decide when something can be repaired vs. should be replaced. A similar dilemma regards cracked or broken ribs. Many people swear by backside rib repairs. They can be great, saving the original wood while making the canoe structurally sound again. But sometimes it's better to simply replace an entire rib. We often use both approaches. It's simply a matter of weighing pros and cons in each new situation.
About the canoe losing its shape because of the damaged inwale, just screw one or more temporary but sturdy battens to the canoe wherever you think weakness might be an issue.