YAYLADAGI, Turkey—Ali Othman is among a shrinking band of Syrian rebels in the mountains across from this border town who face an agonizing choice: accept a settlement with a regime they revile or fight alongside al Qaeda’s Islamist allies.

The Syrian army defector and his fellow fighters say they are weakened and cornered after enduring months of bombardment from Russian forces buttressing President Bashar al-Assad’s regime. Peace talks ended last month without progress amid a major escalation in violence in the northern...