Having taken Cipro myself for over a year, I'd highly suggest trying all you can to deal with this infection head-on.
The only thing I can think of(other than the cautionary side effects) would be to get a good enzyme to control effects of intestinal flora damage, and of course, to keep a very close eye on joint pain. Ciprofloxacin has a well known reputation for tendon damage and cartilage erosion, and so you need to be careful about that.
Other than that, it is a very effective antibiotic for some of the more difficult strains.
PS. While MMS
COULD treat this infection, I'd be very weary of alternative medicines with any serious infection. For example... by identified the strain, you now have the tactical advantage over your infection through conventional medicine. And that's a very good thing!
And so, if it were me, I would deal with this thing head-on and follow through with the Cipro treatment. - After which... once you get this out of the way, you could resume your Candida and leaky gut treatments.
Hope this helps,