Thank you for your responses!
We'll avoid Bern and Neuchatel for now then.
SteveB, thank you in particular for your detailed information!!! It looks like only IR and S-Bahn go through Brugg? So we need to avoid IC... She actually does get off before Enge to avoid the Tunnel and take buses/trams. But to Zurich, this really isn't a huge issue because there are enough above the ground options from Enge to many different areas of Zurich.
Do you know exactly where the other tunnel is by Aarau? Just in case I can find an alternative option to avoid that segment also? But already avoiding a 5km tunnel is a great option, so thank you!
Also, is there a good website where I could find all these tunnels? I looked on sbb.ch but nothing. Wikipedia has a list but it's difficult to navigate through different city names and figure out which lines will go through which tunnels, etc. It would be good to know for future travels to other destinations ;)