Pantload,
Hopefully most people will have no need to diverge from SOPs, but most certainly a good Captain will consider it if required.
Examples I can think of:
1) Departure from an airfield which is below single engine auto land approach minima (haven't mentioned specifics as mine would be different to US regs). You get a engine fire that won't go out. I most certainly would land below minima.
2) My type tells you to close the fuel xfeed if the fuel in both inner tanks goes below 750 kgs. With single engine and confirmed no fuel leak I would ignore that ECAM procedure.
I hope that in my career I have no need to disregard an SOP but I am ready to if the situation dictates. Now pilots who wilfully and constantly ignore SOPs because they know better, that's a different subject.