I've used the Petite Saison d'ete kit, and diced peppers, then added them at the last 5 minutes of the boil, then strained them out as I transferred to primary. I did not experience any contamination issues.
I will say, I was basing this off of expanding from a one gallon recipe offered by another company. Since the original recipe was done in this manner, it never crossed my mind to do a tincture and/or add the peppers in at bottling.
For me, I got the desired effect, although the next time I do something similar, I am thinking of using a variety of peppers from different points on the scoville scale to try and get a bit more depth.