Don't trust a rust converter if you want this to look good for a long time. The rust must be removed.
It could work to keep the outer layer, but you'd have to sandblast 100% of the rust out, which of course requires getting rid of the inner layer. But you're talking about tons of filler, so it would still be best to weld some patches in the holes. If you're welding on the hood anyway, why not get rid of the whole rotten section? There's always more rust than you see. Sectioning a corner from a donor hood in is a tricky repair to make flat, but the advantage is you take in a complete welded seam at the bottom.
Oh, and don't use JB Weld. Just use regular bodywork products. The key is to do the metalwork as well as possible so you only need a skim coat of filler.