Do metal film resistors ever get noisy?
Not generally, to my knowledge, but if they've got damp could be...
I rather disagree with the other contributors above though - I don't think driving a square wave into an unloaded amp should cause any trouble. Obviously it pays to go very gentle with an amp you suspect is faulty, but it doesn't sound like you did anything untoward.
The only danger I can see would be cross-conduction due to the fast rise times - one set of output devices could be turned on before the other set had turned off completely (because BJTs will turn on quicker than they will turn off). Even then, the slew rate would normally be limited at the voltage amplifier stage, so that seems very unlikely.
More likely is accedentally causing or a short or - more subtly - changing something like gounding, screening, stray capacatence etc, and causing an ultrasonic oscillation which could destroy the output devices by the mechanism above.
It's not unknown for op-amps to go "eggs and bacon" (hissing, popping, crackling), especialy is they've been abused in the ways that happen to the inputs of audio amps.
You have proably done anyway, but its worth checking all the emitter resistors, just in case there are more open. Keep an eye on the bias currents, too, and check that the two channels stay at roughly the same current (working on the assumption that you're unlikely to have two channels faulty in exactly the same way). Also check you've no open B-E resistors in the output stage (a potential source of less-obvious problems).
Finally (you're probably waiting for someone to tell you this) you
should really replace the entire bank of transistors to get decent load sharing... however I'm well aware that's proably more than you'd be willing to spend. For practical purposes, I'm sure it will be fine as it stands.