Hi Julia,

Ferrys (coastal liner Hurtigruten and Havila) may get fully booked on the dates you want, so booking in advance is recommended.
The same applies with the trains. There are limited bike spaces, and many people cycle the Trondheim – bodø route in June.

From Tromsø the easiest way to get back south is to fly. You could fly Tromsø – Oslo- Modle maybe for around US$150-200 if you book in advance.
SAS allows bikes to be used as normal luggage (under 23kg) for no extra fee. You can pick up some cardboard bike boxes at a sport shop in Tromsø. Tromsø Outdoors is the best place, but XXL is also good.

If not, as you mentioned, the expensive Havila is an option.

Every other option will be a lot of hassle and logistics.