Ok, you know how some systems have an intake box that is an overflow inside the tank with notches cut out? (Remember, I'mma old skool gal, k? there may be better technology out there that I'm not aware of.)
What if instead of using something like that as the intake only you have another one for the outlet? Let the box fill up, which should allow most of any possible microbubbles to dissipate, from the bottom, and then it flows out in a waterfall. Make it an inch or so higher than the intake's water level so that you're certain of no microbubbles, and I think that you can cut either a sufficient number of, or large enough of an opening notches so as to not reduce flow, but instead just diffuse it.
It's an intake in reverse. Just make it deep enough that the microbubbles have time to come to the surface and dissipate.