Kru, you bring up an excellent concern to water discharge of H limed water. The PH shock would kill just about any aquatic animal until the water was heavily diluted.
I was thinking if you wanted to kill just remaining fish and the pond were mostly drained. If you wanted to try to kill the clover by burning it with lime, I would still loower the pond considerably then heavily dusting the clover with H lime and then watering it down sparingly to prevent runoff.
I know and understand your chemical concerns, but as esshup alluded to, it may be the best choice here. Used correctly, Reward, Sonar, Whitecap and Round-up have proven to be very safe and effective for years. Draining your pond and spraying with RoundUp might be an excellent, low cost solution....buy a small bottle and give a light spray on some clover that is on dry ground and see if it dies in a few days. IIRC, Round up breaks down quickly after application.
