Lets' try and keep this in perspective.
Just because one person has experienced a well-recognised side-effect from a non-steroidal anti-inflammatory doesn't mean that everyone who takes them will.
All tablets cause side-effects. Every decision to prescribe is a balance of benefits versus risks. As is every decision to take an over the counter remedy.
And doctors certainly do not "f" you up when they prescribe anti-inflammatories. Can medical treatments cause problems? Of course they can. Is that the doctor's intention when prescribing them? Of course not.
While it is distressing to hear of one fellow runner's problems with a drug it should not stop people from discussing all the pros and cons with their doctors and making the best decision for their particular condition.
And there is no evidence that NSAIDs interfere with the "immune system".