Driving car is a very good supplement to your JR pass. I also think that driving between big cities is a bit wasting of time and money, but it is worthwhile to drive inside a city. So, I used JR pass last time for "inter-city" travel, and then rent the car to go around in 富良野 and 美瑛.
You will feel the comfort and freedom compared to just taking train/bus or bicycle there (I think riding on bicycle on those two famous route in 美瑛 is not that easy!)
Especially during bad whether (hope you will not encounter this), I saw others holding umbrella and waiting for bus / moving their bicycle in great effort, while I could still go anywhere I like.
You could also consider below for sunflower:
http://www.dosanko.co.jp/hokuryu/himawari.html
You already have a good advantage to move ahead that both of you can drive.
Re the pension, I would go there next time as I missed the view. Besides, including their "main building", in total they could only take 3-4 families / parties, it is pretty quiet and enjoyable.