In FO3 if you drop the FEV into the purifier it's going to kill the entire Brotherhood, so you do have a choice, actually.
Not as much as earlier games perhaps, but a choice nonetheless. You also get to fight Autumn and his supporting troops at the end, so that's not entirely true either. Granted, not as epic as the Master or Horrigan, but it's still a fight.
Both of the scenarios from FO1 and FO2 require embarrassingly poor security; while it's possible in the case of super mutants (although still highly unlikely, and you'd think he'd have decent guards), there's not a snowball's chance in hell you'd get into the main base of an organization as professional as the Enclave without at least getting challenged for name, rank, etc, and in a group that small they'd easily be able to call a false ID on the spot. You can't just walk onto a US Army base if you're wearing an American army uniform, for example.
Furthermore, in a culture that's been isolated from the mainland for nearly 200 years, a foreigner is going to stick out like a sore thumb.
The Brotherhood is in a much stronger position after defeating the Enclave because they have popular support thanks to the purifier and (most importantly) the Enclave tech. This really is huge; they can replace their outdated T-45d and projectile weaponry with the best armor there is and advanced energy weapons. They also got Vertibirds, which is perhaps the most important part; they can wipe the Super Mutants off of the map with Vertibirds. Finally, they have Adams Air Force Base, a safe and mutant-free military installation.
So yeah, it's going to take them a while to get the situation fully under control, but thanks to the Enclave loot they're pretty set by the end of FO3BS.
There's just no way mutants can compete with Vertibirds, let alone Prime when he gets rebuilt, and now that they know the muties are coming from Vault 87 they can just alpha strike it with whatever Vertibirds they captured and cut the mutants off at the source.