Is the small intestine meant to be empty of bacteria?

The small intestine isn't sterile. 

There are bacteria within the small intestine, often of a slightly different mix of species and certainly in far fewer numbers than the large intestine.

There are even bacteria in your stomach: very few, but there are organisms there.

Then as you travel down into your small intestine and further into your large intestine, you get greater and greater numbers of bacteria and a greater and greater diversity of bacteria.