Returning back to the OP's question:
Could this creaking have been a symptom of metal fatigue?
When things make noise, something is getting worn out or broken. But the important question is: Will it break on my flight? The answer is most unlikely. Aircraft are near enough hand made and each and every one is just slightly different from another. So some will make more noise than another. I'll suggest that the root cause of the noise described is the aircraft (slightly) changing shape due to pressurisation. Virtually every airline follows a manufacturer's routine inspection procedure which should identify components which need replacement/repair well before their failure. And even if parts do fail, most aircraft still remain flyable (Aloha, Air SouthWest etc.)