As you are wondering, equipment in the stream itself is likely to be washed away during high water event. Thus diversion is necessary. The water needs to be cleaned of debris that could damage or clog the turbine, anyhow, with some kind of screening mechanism.
People have been taking water out of streams for irrigation and other purposes since forever, and have worked out many ingenious methods of fluming and directing water hither and yon. Miners divert water lots, as well. You have to know that if you divert water into a ditch, it will eventually fill up with gravel and mud, which means that you should make it possible to clean out the ditch every so often. Depending upon the volume, people have used removable boards to dam ditches, removing them and letting the water carry away the debris for cleaning. Some streams require little cleaning, some require lots.
Not all streams can be developed for hydro potential in a cost effective manner, so each case has many unique elements.
Energy Systems and Design has a nice, 10 foot turbine that's worth investigating. There is a turbine called "Powerpal" that uses 5 feet of head and could also work at your site, it sounds like.
In many ways, low head turbines require less by way of civil works than higher pressure systems, and if you have the water flow, may indeed be the best alternative even if more head is available. Practicality is all about cost effectiveness, and so one
answer doesn't fit all situations by any means...
Cheers,
Scotty