When are you going on this trip?
From San Francisco to Crater Lake is only about 425 miles. You could do it in one long day or two short days. If you got there sooner, you'd have more time to enjoy Crater Lake. Is there a special reason why you want to stop over for two days along the way?
If you need two days to rest because some of the family tires easily, why not stay in two different places? If you break the drive into almost exactly equal segments, you could stop at Willows and then Mt. Shasta. About 15 miles south of Willows is the Sacramento National Wildlife Refuge, a waterfowl sanctuary with a drive-through tour. It's not so active now; most waterfowl are there in winter to spring. I've seen deer there before, but was there last week and the biggest wildlife I saw was hares (lots of them).
If you have time for a detour of about 140 miles, you could go from Red Bluff to Lassen Volcanic National Park, drive along the main park road and see some of the major features, and exit the north gate of the park to Redding. Although Lassen is largely a hiking park, you can see one of the most interesting volcanic features, Sulphur Works, with a short walk near the road. It's a beautiful park and very peaceful, because it doesn't get mobs of visitors.
Mt. Shasta seems to make a living off New Age-y stuff, because the mountain has a mystical attraction for many people. It might be a fun place to stay over and browse around.
Willows and Mt. Shasta are not big cities, but they're perfectly adequate and have all the visitor services you'd need. There aren't any parking problems, so those who find it harder to move around won't have to walk long distances.
If you decide to stay over just one night (or you want the midpoint for a 2-night stay), Redding is the place. It's a big city, as northern Sacramento Valley cities go. It's right on the river at a place where it's navigable. There is a nature park and discovery center at Turtle Bay, also a unique foot bridge over the Sacramento River. It's a suspension bridge, and the tower forms a working sundial. The deck is glass, and the entire structure is built on land on either side of the river so no part of the bridge is in the river itself. It's bicycle and wheelchair accessible; on the far side from the nature center is a wonderful botanical garden.
West of Redding, maybe 12 miles, is a ghost town called Shasta City (NOT to be confused with Mt. Shasta on I-5). It's from the Gold Rush era although it isn't in the Sierra. The main street is Hwy 299 and there are many old brick buildings. The museum has exhibits about the Gold Rush, a jail with a resident ghost, and a gallows which you can explain to the kids as you deem appropriate.