Endotoxins, mostly Lipopolysaccharide released by bacteria as they die, appear to be broken down by UV treatment. So including a UV lamp after your air filtration system may mitigate this. Another option would be to use water to filter your air, like a giant bong, allowing you to dispose of the water as it gets dirty. Lastly endotoxins can be baked out at 250-300 deg C, so a carbon filtration system could be periodically baked out to be reused. I doubt any plastic fiber hepa filter could withstand such temperatures.