You're right. You can't put her in a bubble! I know it looks bad now, but it sounds like she'll heal. It's amazing how flexible and durable kids' bodies are. God knows that kids are supposed to get hurt!
Remember the phrase, "Fall off the horse, and you better get right back on again?"
That means you MUST encourage your daughter to get back on that bike as soon as possible. The longer she avoids it, the tougher it will be to overcome any fear of riding. The adults around her also need not to make such a big deal about her riding the bike. She'll get anxious and use your fear as an excuse not to try again. Riding bikes is such a crucial part of childhood (teaches independence, adventure, motor skills, etc.)--wouldn't you hate to have her miss out on it?
She's definitely learned her lesson (about avoiding mud patches in the future). So has your husband (about helmets). You can remind her that if those who never make mistakes never learn anything new.
That goes for us grownups, too.