1. The Bhagvad Gita is commonly understood to be a discussion of appropriate duty. In this case, Krishna's argument was it is Arjuna's duty to go to war, considering that all other peaceful solutions had been explored and rejected by the Kauravas (Arjuna's opponents)[2]. In fact, Krishna himself had acted as peacemaker, and asked Arjuna to take take up arms only when that failed. The use of the Gita by Indian Nationalists fighting for Indian independence from the British has to be understood in this context.
2. Doniger says that the war was "lawless", but the Mahabharata war was an attempt at a "just" war, as understood in its contemporary context. Deviations from just behaviour are noted and held up as examples of unjust behaviour.
3. The so-called "Doomsday" manifestation of Krishna is in fact him showing his universal form, which is supposed to be beyond the capacity of ordinary humans to visualize, which is why Krishna had to grant Arjuna divine vision to be able to comprehend it. Doniger's use of the Abrahamic term "Doomsday" is loaded, because the understanding of comprehensive destruction or "Pralay" [3] in Hinduism is very different. Sure Doniger understands the difference, since she is a professor of Religious Studies.
4. She seems to be applying guilt-by-association by tying the Gita to the RSS and the assassination of Gandhi, and she criticizes Richard Davis for being too respectful of Hindu understanding of the Gita. Overall, the impression is that her anti-Hindutva agenda is spilling over into being an anti-Hindu agenda.
[1] http://creative.sulekha.com/risa-lila-1-wendy-s-child-syndro... [2] http://en.wikipedia.org/wiki/Kurukshetra_War#Krishna.27s_pea... [3] http://en.wikipedia.org/wiki/Pralaya