The weapon is light and easy to use, even for the elderly, which is why it became associated with women and wives, and is still a popular martial art for women, like kendo. When a woman married into a family of warriors, she had to bring her own Naginata. After they became the equivalent of housewives for their Samurai husbands, they would indeed stay at home, and they had their own Naginata to protect their family.
There have been famous women Samurai, before the confucian concepts of the subserviant, obedient wife took hold. Even so the Naginata became increasingly associated with women. The weapon was originally used by guards, not Samurai; the reason for its shape is to allow a soldier on foot fight someone mounted on a horse. In 1550, when the gun came to Japan, it replaced the Naginata in warfare.
Ninja were spies, they were trained for stealth which made them excellent for gathering information or stealing valuable items from enemies.
Tokugawa Ieyasu was the first lord that hired ninjas, his favorite was a man named Hattori Hanzo (yes, the name that was stolen for the sword maker in Kill Bill), who was not a not a killer. It was the Samurai who were sent out to kill people, not the ninja. Your sensei's disgust for ninja seems misguided; they were spies, not assassins. Also, the ninja disappeared altogether during the
Edo period, and only resurfaced again as entertainment. Doing a google search for "ninja" on the internet shows just how many misconceptions about ninja there are in the western world.