One thing I'd like to address here is that this question inherently implies that House MD is somehow representative of real medicine. This is a topic I've had to breach with hundreds of students over the past 10 years when I was still teaching chemistry...

House is about as far from real medicine as you can get. The number of times his medical license would have been revoked is very high. He uses questionable methods and skips over very basic diagnostics on a predictably regular scale. The show puts that in the light of him being outspoken and clever, but in real life that would just be bullheaded stupidity.

Don't expect there will always be a "real" explanation for what he's doing, because there often isn't. Some comments here have brought up subdermal birth control for the scene in question, and maybe that was the intent... But there's a dozen other ways that diagnosis could have been confirmed that are much more scientifically sound.

Medicinal chemist here.

Two things: A full immune response is usually the body's response to biologics, not just random chemicals. The vast majority of marketed drugs are not biologics. There are certainly drugs that are biologics, though, so it's still a fair point of quandary.

The body does try to eliminate all foreign bodies, whether they're biologics or not. There's multiple areas of drug design that are dedicated to getting around this via either small changes to the chemical structure to combat digestion and enzymatic breakdown, clever formulation to assist with rapid transfer into the body... And most likely both of these things.

The drugs you see marketed usually don't have problems with immune response because they'd never see the light of day on the market of they did. Many drugs get pulled in clinical trials for adverse effects of various types, which is why you don't see them.