Lens flare in interior pictures is a real problem that I am not sure how to prevent/minimize. It seems flare is at its greatest when the camera is aimed directly (straight) at the window/light source. Also smaller windows tend to create more flare. How is everyone dealing with this problem?
First, by shielding the lens from as much of the non-imaging light as practical. Deep (petal shaped) lens hoods are best, but few are optimal because it's not a practical shape/size and it assumes a fixed focal length.
Second, by the choice of lens. Lenses with fewer elements/groups and with high MTF at low spatial frequencies, and
good coatings, and
proper interior reflection baffling (including blackening of lens edges), will be less sensitive to glare. Modern multi-layer coatings (some of which have nano-structures) are often much better than old designs.
Third, anti-reflection treatment of the camera (and/or mirror box) interior, which is part of the camera design.
Fourth, coating of the IR filter in front of the sensor, in other words sensor assembly design.
Fifth, software solutions that are able to adaptively deconvolve an image with the Point Spread Function (PSF) of glare. Very few commercial solutions exist, which leaves proprietary solutions, or generic ones like raising the Black point clipping (perhaps restricted with a shadow selection mask).