Worth JR pass to Kyoto return from Tokyo?

I will be in Japan for 9 days and plan to get a 7 day pass but is it really worth it or should I just get the bullet train separately and buy local train tickets?

Use Hyperdia (hyperdia.com/en) to calculate your train fares and decide if the Pass is worth it.

There is a new pass becoming available next year that includes travel between Kyoto and Tokyo, runs for 7 consecutive days and is cheaper than the nationwide JR Pass. Information is available in the link about new passes on the front page of this website. The pass will be available from April next year.

If you also plan to go to Osaka, Himeji, Hiroshima or basically one extra trip, then yes it is worth it.
If you are also going to travel back to Narita Airport within the 7 days then also yes it is worth it.

The difference is only 2310 yen.

For me I would get it just for the flexibility of changing plans as I go within the 7 days.

Hope this helps!!
Have Fun!!

Simply going Tokyo-Kyoto-Tokyo would still leave you short in recouping the cost of a 7 day pass. But if you take the Narita Express from Narita to Tokyo at least once you would break even. You could add a lot more savings by going to other places like Himeji or even Hiroshima.
Since you will be in Japan 9 days as you say, a cheap way to get into or out of the city would be the 1000 yen bus.
http://accessnarita.jp/en/home/

The Tokyo-Osaka Hokuriku Arch Pass was mentioned as a cheaper way to get from Tokyo to Kansai, but it is also slower - you will need over 2 more hours to travel the distance each way.

A better option might be the Japanican discount bullet train tickets. You can get into Kansai even faster since it allows you to take the Nozomi trains, but on the downside there are no free advance seat reservations.
http://www.japanican.com/en/tour/detail/VJOPENTK1/
It also includes a Kyoto sightseeing one-day pass.