Well, only few percentage of people who say "Islam comes first" would act like this. Maybe %2, %3. Like the ones who joined ISIS and record videos threating Turkish Republic. The big majority thinks treason and unrest (fitne) is also sin, so they would never act like that even in name of Islam.
Also there is a rule (ulu-l emre itaat) which prevents muslims uprise against state. Because of this rule, Turkish muslims never uprised against state even in hardest times when opression against religious people was so intense (28 Şubat and following years) (Big uprisings in first years of Republic were ethnic, religion was only a cover to mobilize people)
Shortly, even Turks who say "Islam comes first" would support their nation and state if theoretical situation in your post becomes reality.
PS: As a Turk and muslim, I say "Islam comes first" too. But it's not because I don't give enough importance to my nation but because of fact being rationalist. If you believe in a religion which warns you about eternal hereafter life, you should normally give more importance to eternal life. Nation is affecting only this life, but religion affects both, that's why I think religious identity comes before nationalist identity.