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If the Armenians were the undesirables you, and many others, obviously, say that they were, why is it that in the 19th Century Ottoman Empire:

29 Armenians achieved the highest governmental rank of pasha,
22 Armenians became ministers, including Ministers of Foreign Affairs,
33 Armenians were elected to the Parliament,
7 Armenians were appointed as Ambassadors, 11 as Consul Generals,
11 Armenians served in universities as professors.

Why where were 803 Armenian schools employing 2088 teachers with over 80,000 pupils within the Ottoman Empire in 1901-2?

One would hardly allow such policies for a certain group if one's policy was the destruction of that group.

The Ottoman Empire, with the exception fairly limited massacres in the 1890's, was not the perpetrator of the sweeping campaign of massacre, deportion, "resettlement"- genocide. In the 1890's the Sultan instituted fairly limited massacres and crackdowns. This was largely a reactionary movement to reforms of previous years, and indeed a reaction to the very statistics you cite. Armenians were rising above their traditional status, and to the government at least, this was a threat. For the Sultan it was religious based, for the Young Turks it was more "secular".

Now, let us come to the Young Turks, the perptrators of the genocide (or suppresors of the evil Armenian revolutionaries...). They come into power, what do they want? A state composed of Turks, for Turks. The Armenians are not Turks, what's worse they hold economic power, and are rising politically and culturally. Perhaps they posed a real threat to the Young Turk's dreams (though that hardly gives a good excuse), but probably not: for the reasons you cite- they were good citizens, and the Ottomans had treated them fairly well- why rebel? But authoritarians and their ilk are rarely masters of morals or reason.

Please understand I have nothing against the Turkish people. Indeed, they were often resitant to the perpetrations of their government, and Armenians found much better friends in Turks than Jews would in Germans. But why defend a government that so obviously commited awful acts?