To try and address your specific concern:

To me, the "difference" between "diabetes medication" and "anti-diabetes medication" can be likened to the "difference" between ""medication for diabetes" and "medication against diabetes". Although the terms for and against appear to be polar opposites, they are in fact frequently used to mean the same thing to all intents and purposes.

diabetes medication = medication for diabetes, i.e. medication appropriate to diabetes, medication used in relation to diabetes, medication designed/intended to treat diabetes

anti-diabetes medication = medication against diabetes, i.e. medication effective/working against diabetes, medication combating/counteracting diabetes

The same thing applies to your TB treatment/anti-TB treatment example.

In medical terminology, the prefix "anti-" generally means against.

Anti-: Prefix generally meaning "against, opposite or opposing, and contrary." In medicine, anti- often connotes "counteracting or effective against" as in antibacterial, anti-infective, and antiviral. Sometimes medical terms containing anti- take on new meanings as has occurred with antibiotic and antibody. As a prefix, anti- may be shortened to ant- as in antacid. "Anti" is the Greek word for "against."
http://www.medterms.com/script/main/art.asp?articlekey=25282

You may find the following paper of interest. It discusses the use of apparently negative prefiixes in medical English and how they affect the root term. One of them is "anti-". Some extracts:
In medical English it means “intended to prevent something from happening” or “to destroy something harmful”, e.g. anti- cancer, anti-infection, anti-seasickness ...
the prefix is used in chemical and medical terms with the meaning "counteractive, neutralizing, preventive of" ...
http://www.bmj.sk/2007/10845-15.pdf