I hear ya. Even today, I think being Catholic has a certain stigma to it in politics. I was raised Catholic as well.
As to your points, I think we're on the same sheet. What you seem to be saying in essence is that the apostate muslims are more prone to simply living in peace with others. If so, then I agree. But you must remember, and the same stands for Christianity although one's a faith in God, the other is a faith in a made up god, that for either one, you can't simply deviate what it is from its foundational underpinnings.
Eg., Christ is the foundation of the Christian faith. Disprove either his existence, his resurrection, or his ascension, and you've successfully disproven Christianity. Far more brilliant men than us have tried, some animously, and have been turned towards the truth and light of the gospel. Regardless, it's been twisted and contorted today, and that displeases God. What society does with it can be independent from what God looks for in us.
Islam's book is the Koran. Unlike the Bible, in which Jesus Christ commands Christians to live in peace and do unto others as they would have done unto them, and love others, the Koran calls for the domination of non-islamic peoples and what essentially boils down to forced conversions "or else." While Christianity values women inherently, Islam and the Koran place women in a lower class than men essentially. It does the same for non-muslims.
So while it's easy to deal with apostate muslims, it is nearly impossible to deal with fundamentalist muslims as you say. The big problem is that you can't distinguish between the two outwardly reducing any such efforts to a guessing game. Yet, by allowing muslim fundamentalists to integrate into a society, unless one guesses with 100% accuracy, an extreme unlikelihood, troubles are bound to occur.
As well, the root of muslim issues, namely terror and general societal won't ever go away as long as they're in the source tome for Islam. Christianity is the opposite. If everyone Christian adhered to Biblical teaching, then the world would be a much better place.
So "deviant" Islam is good, fundamental Islam is bad. Deviant Christianity can be "good" in the same sense that it likely will not cause societal woes of the magnitude and breadth that fundamental Islam will. It may cause moral woes and issues, but those are not of the variety that necessarily threaten the lives of others. Either way, fundamental Christianity does no one harm, and in fact is good in spite of people that think morality is somehow bad.
The bottom line, it's futile to hold out expecting the entire Islamic community to become apostate to one degree or another. It'll never happen, and the risks are far too great for societies that desire to remain civil to allow Islam to spread to the extent that it already has in many nations.
Unfortunately, as has been the case throughout history, even on this issue, what isn't clear to many today, will become crystal clear "tomorrow."