Ninjas are a defense class, rather than a resistance class. /Kin will do better with resistance type pets.
You'll be happier with anything that adds defense. Jounin start at 15% def, before you even begin using enhancements (which go on "Train Ninjas" instead of on the actual power itself) 45% is the "soft cap" where only 1 in 20 attacks from an ordinary enemy can land. Decent enhancing, plus slotting the 2 +def procs can get you up to 35%, but if your secondary adds anything, that will probably get you over the top to 45%. Then your pets are nigh indestructible most of the time.
Also Jounin can use "Achilles Heel: Chance for resistance debuff", which will indirectly add to their damage, and that of any party members. A great compliment to /Kin if you choose to stay with that.
I agree, however, that it would be cool if the MM could have a sword. At present the best I can do is give her a mace. 😞 However I am able to get over it because the ninjas themselves look so cool!!!!!