While some of the Nepalis may well have been there "illegally," bear in mind that the law was changed retroactively, and enforced with none too much solicitude for the rights of those deported.
The communist (Naxalite) movement based in NE India did make "incursions" into Bhutan (and were ultimately repulsed), and probably had a lot of support from the general Nepali-speaking population--and they had the right to be communists, no?--but this is a fundamentally different issue. The average Hlotsampa did not take up arms against the government.
Too often, Western dharma practitioners value the "preservation" of Tibeto-Himalayan culture above the human rights of others whose cultures are less attractive. But culture changes anyway. If things had been a little different, Bhutan might have embraced the principle of respect for diversity alongside their much-vaunted democratic reforms.
Dhimal describes the day in June 1992 when Tshring Togbe, the district magistrate, arrived in Lali accompanied by Bhutanese soldiers. Togbe called the villagers to assemble and then announced over a loudspeaker that they had seven days to pack up their belongings and leave the country. He spoke to them in Nepali. When a few of the peasants protested, an army officer shouted, “This is a hunting ground, and we can take you like monkeys.” Dhimal, his wife and five young children decided to leave. They had heard of people being killed in neighboring villages.
http://www.hrw.org/news/2008/01/31/bhut ... -cleansing
“The army took all the people from their houses,” a young refugee told me. “As we left Bhutan, we were forced to sign the document. They snapped our photos. The man told me to smile, to show my teeth. He wanted to show that I was leaving my country willingly, happily, that I was not forced to leave.”
Look what you are supporting. Are you not ashamed?