He was built with an order, a compunction, to ensure the continuation of organic life in the galaxy; not any specific race or species. His logic says that another AI created by these organics may not share his orders. Some may be peaceful (the geth), but some may not (every other killer AI). Even if there's a 1% probability a killer AI grows powerful enough to overtake the galaxy, that's a meaningful enough probability to act first (especially to a being that can live forever).
Maybe I totally missed the logic here but
Why was The Catalyst's solution to the task preserve all life to have the reapers wipe a good chunk of it out every cycle?
Consider it this way, a tree growing near power lines. If you let it grow, it might hit the power lines and burn the entire thing down, never to grow again. If you prune the tallest leaves and branches, it can regrow. This is what the Intelligence is thinking. There's also the aspect that he feels he's 'preserving' those species 'in Reaper form'. Tantamount to building a house or furniture out of lumber cut from that tree.