Most people are usually allergic to casein or lactose when it comes to dairy. I hadn’t heard of a whey allergy, but any protein can cause problems in susceptible people. It’s a shame, because whey protein has been shown to help with leaky gut, as well as some other health problems.
As for hormones, rBGH is illegal in some countries, e.g. anywhere in Europe. Oestrogen content is apparently 34ng/8oz of milk, compared to the 136,000ng/day men produce. 4oz cabbage has 2,700ng and 1tbs of soy oil has over 28,000ng, although these may behave differently to animal sources, but probably explain stuff like this. The oestrogen/progesterone ratio is supposed to be good in milk anyway. This page has the following about antibiotics.
Antibiotics may be given to prevent or treat disease in cattle. A “withdrawal” period is required from the time antibiotics are administered until it is legal to slaughter the animal. This is so residues can exit the animal’s system. FSIS randomly samples cattle at slaughter and tests for residues. Data from this Monitoring Plan have shown a very low percentage of residue violations. Not all antibiotics are approved for use in all classes of cattle. However, if there is a demonstrated therapeutic need, a veterinarian may prescribe an antibiotic that is approved in other classes for an animal in a non-approved class. In this case, no detectable residues of this drug may be present in the edible tissues of the animal at slaughter.
I don’t think these things are optimal, but I think they get blown out of proportion or outright lied about by naturopaths and other pseudoscientists. I think the more pressing issue is whether or not the cows are pasture fed, since this means more of the nutrients that make dairy so good. Many organically raised cows are just pounding wheat grains without the pesticides.
If you want to avoid whey, I think Greek yoghurt would be good because it’s mostly drained away (hence the thickness). You could try draining the whey from your kefir with a cheescloth to make cottage cheese. There are instructions on Dom’s kefir site. There’s a chance another factor caused your issues though. Whey protein is extremely insulinogenic, for example, or maybe you can’t digest lactose properly and were feeding candida. Have you tried “whole” kefir to see?