Sounds like a detox or herxheimer reaction.
You are using kefir from Real Milk Grains and not one of those weird pseudo-kefir enhanced buttermilk products?
I see recommendations to continue taking a few tablespoons a day and work up from there if you can tolerate it. Kefir is regarded as safe and the beneficial organisms in it have never caused food borne illness. I suppose it is conceivable that badly mistreated milk grains might not culture a contaminated milk properly. Its hard to comment on something like that.
The microflora in kefir are dominant organisms and very hardy. Otherwise they wouldn't have survived as a Grain for a thousand years.