I'm not certain that complete engine replacement is still the MoCo's only repair option. In fact I'm quite certain that at least one person reported having just the crankshaft replaced by his dealer.
If you prefer a complete engine versus a dealer repair, I would suggest that you let your dealer know that you will be contacting the MoCo to request a full replacement, enlist his support, and then call the MoCo direct. As for which method, replacement or repair, would be the best way to go, that is a crap shoot. If your dealer has a really good engine tech who can be trusted to do things right, it might be better in the long run to let him rebuild the engine with a new crank that they send out to be trued and welded. You would have to pay for that, since the MoCo won't, but it would be well worth the cost IMHO.
Jerry