A pond that size, and given the root issue... it may make sense installing a rubber liner. It may be a good, solid zero leak fix for you.

If it were me, I would drain it, clean it, till in some polymer sealant, fill it, and then apply a little more polymer sealant to the water. You have nothing to loose, and it probably wouldn't cost that much. The rubber liner would be expensive, but be fairly certain of zero leaks.