Of the available methods of treating IRB, chlorination is the least expensive that works well. Now, if you come up with something that is as reliable and less expensive, all well and good. Maybe you'll make a mint. You could probably use a ceramic filter, but it would likely clog up fairly quickly and back flushing it would waste a fair amount of water. A good ceramic filter can block many viruses, so bacteria should be easy. They are not cheap if you want any decent flow rate, so that leaves you back at something that works, won't detract from the flow, and is still fairly inexpensive. You can beat your head against the wall as much as you want...at least right now, I don't think you'd find anything else that would work as well.
Microwaves would be absorbed more by the water, and unless you heated the flow enough to kill the bacteria, just passing them by probably wouldn't work well. It's fairly expensive to generate microwaves with enough energy to do the task, and leaks could be life threatening. The water bath would damp any resonant frequency of the bacterium, so I think you'd have a lot of trouble zapping them in that way. Microwaves heat water fairly well because they are tuned to vibrate the water molecule. I don't think you'd get it to vibrate the bacteria.
UV needs dwell time to work well, which you won't have. Take a neat hiking UV water purifier, it takes over a minute (with the small UV lamp) to purify a liter. Getting a bright enough array to do it to your water as it flows past would cost a fortune, and the bulbs only last about 1000 hours. Get out your checkbook, and buy stock in the utility company.