In Missoula, I'd say Big Dipper Ice Cream is a must. Depending on what type of kids they are, they might also like the Smokejumper Center out near the airport. Outdoorsy types might enjoy a
Montana Birding and Nature Trails.
Does the presence of Going to the Sun Road on the list mean that outside of Missoula is fair game?
I live on the Pintler Scenic Loop in Philipsburg. We have
Granite Ghost Town here just outside of town (less touristy, more gritty/rough and tumble looking than Garnet) as well as Doe Brothers Soda Fountain (recently sold, but open under new management), and the
Sweet Palace candy store. If you're willing to go a little off the loop, you can do the sapphire mining thing at
Gem Mountain and also hit Skalkaho Falls. You may be able to take Skalkaho Pass over or back, depending on how much or little you think the kids would be into a pretty scenic drive. Also on the scenic loop is a less known feature in Anaconda called the
Copper Chute- a 40 foot slide ending in a sand pit.