I am suffering from oral thrush and eczema (eczema likely candida related) and I recently started making my own kefir but upon researching the common bacteria found in milk kefir, I discovered that it contains C. krusei. Candida krusei is a pathogenic fungus that is known to be resistant to fluconazole (which I have taken in the past for my thrush to no avail). In addition to that, it also contains C. famata, C. lipolytica, C. inconspicua and other candida species. So, should I be drinking kefir when I have candida overgrowth?

These Candida species are only an issue in severely immune compromised people.  They are not pathogenic is people with intact immune systems.

The growth of these Candida species and a person's own Candida is actually controlled by the acids produced by the normal flora o the body and in fermented foods like kefir.  Just make sure that the kefir has been fermented long enough to destroy most if not all the sugar in the kefir first.

Also, what is good for treating oral thrush?

The kefir will work.