Also, I've found that when you have a sore throat from a cold it's good to let them pipes sit until you're feeling better. Having a pipeful with a mild flu can really aggravate the illness.
ale: Tar and smoke are not the best healers.
As for throat hurting from smoking I pretty much agree with what has been said already. Try to keep the pace down and do not inhale too deeply.
Drinking a soothing cup of tea with a pipeful will also ease the consequences in addition to being pleasant in itself. Camomille works best for softening the throat but a cup of quality Earl Grey tastes heavens! For Latakias, coffee works best, of course. When unable to make tea have a glass of warm water nearby and sip it every once in a while. Will also bring out new layers of taste in the tobacco.