Yeah, Apollo's a Superman ripoff and MN'er is a Bats ripoff, but they're a lot different and cool in their own way (MN'er in particular is a complete badass)
Flash is the JLA's only hope here (as demi mentioned). But an evil Doctor (he stole the regular Doctor's powers at one point) once put himself back together after being run through by Swift, so it might not be that easy to kill him. Also, when Jenny Fractal (Jenny's Q's evil twin) was briefly "destroyed" by the good Jenny she put herself back together at an atomic level. Presumably, Jenny can do the same thing since their power sets are the same. Even Flash can't mess with that kind of power. Beyond that, regardless of whether or not The Doctor's alive, they have a universal-level matter manipulator, and 2 if The Doctor's around...and the regular members can go toe-to-toe easily with their DC counterparts (MN'er/Bats, Apollo/Supes, Engineer/GL, etc.). The Doctor can also time-travel if he's around, so there's another cheap win.
The Authority might be a bit cheap at times since Doctor and Jenny have some ridiculous powers, but they're beyond any of the normal teams in comics in terms of sheer power (The Defenders might stand a chance, but even that's unlikely).
P.S. I'll have to get my hands on some of that new stuff whirly...the last thing I read of The Authority was the Fractal story arc in Volume 2...not sure how much more they've had since then.