When making cheese (e.g. Halloumi) from non-homogenized milk, are the dangers in non-homogenized milk neutralised?
You are indeed mixing up different things, as Tetsujin mentioned in comments. 

When the milk comes out of the cow, it is an emulsion, but not a terribly stable emulsion. Also, it has bacteria in it - ideally only the milk acid bacteria from the cow's udder, but it can also have pathogens from either a sick cow (usually things like listeria) or from being contaminated, e.g. e. coli from the cow's fecal matter. If you leave it sitting around, even at fridge temperature, the emulsion will start separating, with the milk fat swimming to the top, and the milk will start to either turn sour or spoil, depending on which kind of bacteria prevails. 

Modern consumers don't want any of these to happen, and modern producers and handlers don't want to have to sell the milk within a couple of days of milking. So milk is typically processed in multiple steps. Some of them are intended for pasteurization (killing bacteria), others are intended for homogenization (preventing the separation of milk fat and whey). There are many different processes for each of those two goals, and a producer can apply one or more of them - and the producer can also decide to homogenize without pasteurizing, or the other way round. You can also consume raw milk, if you can find a source - they are differently regulated in different legislations. 

Now, to your question. The important part for your safety is not whether your milk has been homogenized, but whether it has been pasteurized. If you make your cheese with non-pasteurized milk (no matter if homogenized or not), then che cheese "inherits" the risks of the milk. If you make it with pasteurized milk, it again inherits the risks (or lack thereof) of the milk. To answer very literally, the cheesemaking process doesn't turn raw milk into safely pasteurzied milk.