If you use your bike at all, you are damaging it in some way, (friction and wear in many places).
As long as you keep it under red line, I don't see an issue with using engine compression for braking. Of course, you have to modulate your rear brake pedal pressure to keep an even braking effect. I wonder if you're talking about using clutch friction, slipping it during decel. That will certainly wear out the clutch faster. If so, for street conditions (not racing) leave it in gear, using engine braking.
For example: say you are cruising at 60 MPH, top gear, and need to come to a stop. Back off on throttle and use engine breaking and that top gear, until the engine gets at or near idle RPM. Then pull in the clutch and go down several gears to first. Complete the stop.
Bikes were meant to be used for fun and inevitably get used up in the process. If your technique reduces enjoyment/performance, why trade the fun for some small amount of longevity? They aren't going to last forever, no matter what you do, short of a museum exhibit. And, if it IS a museum exhibit, who cares if it is worn out inside? It's just eye candy.
IMO
Cheers,