Wow, Thank you Andre for the detailed response. This is why I love Flyertalk!
It seems the half fare card is the way to go assuming we do get to visit one of the mountain tops. The fare alone to Jungfraujoch is 184CHF.

I was poking around the SBB site. I tried a dummy booking from Lauterbrunnen to Zurich. I noticed that it stops in Interlaken and Bern. I also noticed that the connection times are very short like ~5 minutes.

If we miss the connection, is it OK to take the next train with no additional fees? Or if want to walk around Bern for an hour or so to see the city, can we take any train or are tied to the connection that was originally purchased?