Health was a major consideration when I was first exploring pipe smoking. I'm an advocate of making properly informed decisions, so I did and continue to do a fair amount of Internet research.
There is absolutely an increased risk of cancers (particularly of the mouth and lungs) and other smoking-related diseases, but a couple bowls a day puts that at a fraction of the risk of a pack-a-day cig smoker. Additionally, there's a strong dose response relationship, meaning risk increases the more you smoke. Risk increases the more you inhale, as well.
I smoke only a few times a week, which balances my desire to enjoy pipes and tobacco with minimizing health effects, both chronic and acute. It's up to you to decide how to balance those properties and any others you may consider, such as financial cost.