From what I have heard and read, the Jonang school is considered a minor school as during the time of the 5th Dalai Lama, when a lot of Jonang monasteries were closed down, most of the practices either lost or incorporated into other schools. Of the most important teachings now existing of the school is their practice of the Kalachakra Tantra that is most prevalent.
For the purpose of the political unification of Tibet, this was done, according the Dalai Lama's wishes, but it was done so at a very high price, the near destruction of a school that influences and was incorporated into each of the four major schools of Tibetan Buddhism to some degree or another.
On another note, Yes, the Bon religion is not Buddhist in origin and of course included animal sacrifice in the past, but the tradition as it stands nowadays does not adopt this view of practice due to the influence of the Buddhist notions of karma and compassion. I know a few Bon practitioners in the west, and they abhor such practices, they prefer to call themselves the New Bon.
This being said, my own opinion is that the government, as its structure stands now, should be representative of all it's spiritual traditions. So Bon, in my opinion SHOULD be included in the Tibetan Goverment, because there are still practitioners of that specific religion in tibet and also in exile, despite the fact that they are not Buddhist. However this is the same for the Jonang School too. Why restrict other traditions in such a manner?
But we have to ask ourselves, if some of us are not Tibetan or live in countries who's governments do not represent Buddhist perspectives, or who don't even accept that some of their citizens are Buddhist, or who marginalise Buddhism or certain schools or traditions such as our of practicing Dorje Shugden, shouldn't we be doing something about that as well?
After all, the Dalai Lama has accepted them as a valid school, which can be taken as steps to ensure their preservation. But the Jonangpa's are now asking for seats in parliament.
I cannot but think that surely what the history of Tibetan government and all of world history has shown is that religion should not be involved in politics any longer.... this is my opinion, but how feasible this is, I don't know. I'm a farfetched dreamer to say the least, but religion has been used by too many people to justify political movements for too long, all over the world. Governments should be set up in free democratic ways, free from religion but should be represented by only one or two ministers who represent the faiths of all that countries citizens in a fair manner. Maybe in another universe....