(HUGS) Hun, sometimes my Lo will stir or cry between 45mins and 1hr10 when sick which is usually light sleep for him. TBH I am a bit of a soft touch and I just usually go in and give him a cuddle, BF or help him back to sleep if I need to. That said when my LO wakes mid nap he gets really upset and he only does so when ill so we tend not to end up with prop issues unless he is poorly for quite some time.
If you think he can/will resettle on his own I would leave him to try to do so, esp if you know interfering could make it worse. You could try sneaking in at 40mins os so and being there when he stirs to help him through the transition, but again this could make things worse. Its tough when they are ill, I tend to just do 'whatever works' and if you end up with a shor tnap just offer another one late PM or EBT maybe to prevent OT.