'Whereas' as conjunction between main clause and subordinate clause?

There's nothing wrong with using whereas as a conjuction. The Cambridge Dictionaries Online site has a good example:

compared with the fact that; but:

In Los Angeles, a chief cause of this pollution is paved-road dust, whereas in San Diego, it's smoke from fireplaces.

The Oxford Advanced Learner's Dictionary offers a few more:

used to compare or contrast two facts

Some of the studies show positive results, whereas others do not.

We thought she was arrogant, whereas in fact she was just very shy.

However, in your particular sentence, the usage is quite strange. When used to separate two sentences, whereas should be use to compare the two statements, whereas in your sentence it's simply providing additional information. Since would make a lot more sense here:

As a model system we consider a mutant zombie hoard, since the vast majority of zombie hoards fall into this category.