Most Muslims do not kill or punish homosexuals. They tend to ignore them. Just as Christians tended ot ignore them unless they make a big deal of it, as Oscar Wilde did.
The fact is, Islam is as intolerant as fundamentalist Christianity, but there is no solution to the problem that Islam exists.
There is very little chance that it will be reformed from the inside, and even less that it will be reformed from the outside.
Unlike Catholicism, which has a pope, Islam has no single leader to say "Who am I to judge?"
Extermination is out of the question. Not only is it highly immoral, it is ineffective: Hitler did not do away with the Jews. The Turks did not do away with the Armenians, and have never resolved their differences with the Kurds, who are fellow Sunni Muslims with different languages (there are a variety of Kurdist languages) slightly different customs and fashion sense.
So even if we ignore the fact that genocide is morally wrong, extermination would likely just create martyrs and would be unsuccessful.
Islam will become irrelevant to a majority of Muslims, just as the Roman Catholic Church has become irrelevant to many Catholics, who now practice birth control, get divorced and have abortions, no matter what the Holy Mother Church says.