I wouldn't prune it more than 1/3 of the plant.... that is a good rule and it should leave some green for photosynthesis and the plant should recover next year if you take care of it. :o)

....."The problem is that the needles that have stayed green and healthy are growing closer to the branch ends than to the trunk of the plant, so if
I prune it back, I will end up with mainly brown dead looking stumps." .....

I would let those continue to grow and develop for now in helping sturdiness and giving a strong visual impression. Once those become more
mature it will sprout out new growth all along these branches.

As for leaves turning brown, that may indicate that the drainage is insufficient or an under/over watering issue.

{{gwi:12058}}

Maybe just pinch out the growing tips to encourage new growth back along the branches.

How old and what size is your Rosemary? For the time being I would do nothing other than bring it in and let it adjust to indoors. With leaves only on the tips and the lower ones withering you indeed do have a problem. I'd give the roots some water and do not mist the plant or prune anything...yet.

Give it some time to adjust and for the roots to hopefully

revive and get circulation going better to the lower (older) part of the plant. That the newer tips have leaves seems to indicate that there is some circulation moving. Some diluted vitamins may be helpful too.

Hopefully it will recover. Clearly the plant had problems this summer/fall. I am in a much colder zone and I dug up my Rosemarys yesterday when temps threatened 15 degrees. They are very robust...so something wrong happened to it.

Rosemarys are strong growers. When you plant in a pot you need to check the roots throughout the season to see if it's root bound. When you lift your plant out of the pot and the roots are showing or circling it will start to decline. It's too late to top prune or root prune now that the plant is going into dormancy. In early spring (March in your zone)lift your plant out of the pot and cut off a couple of inches from the bottom and with a serrated knife slice some off the sides and replant in new soil and a larger pot. Don't prune from the top until you see some new growth. When you grow herbs move them to larger pots or root prune and return them to the same pot and you will have happy, healthy plants. I have large stock plants of rosemary that I have done this to for 10 years.

What herblady49 says about dormancy may be true, but I'd still consider doing what greth suggests and just pinching out the growing tips. You'll get a few little shoots growing along the stems as an "insurance policy" against the whole stem turning brown, at which point it will be too late to rescue the plant. Gently remove the needles that are entirely brown and dead and keep the plant in a cool and humid place with plenty of air circulation during the winter.

Thank you all for your advice and encouragement. I will follow the advice given and will let you know (next spring) how it turns out.