Would I it be a bad idea to buy a box of early church cards just to get Shipwreck?
Yes and no. Yes, because there is no guarantee that you'll get one (I have opened probably 3-4 boxes worth of EC packs, and despite opening 4 Loves, 4 Evil Sacrifices, and 3 False Prophets, I have yet to open a Shipwreck). However, it's not necessarily a bad idea because if you have the money available, EC is a set chock full of good, playable cards, and the packs also come with six tin cards. So even if you weren't able to get a Shipwreck, you'll have plenty of good, tradeable cards (or if you don't have them, cards that can be nice adds to your collection). And of course there is a decent chance that you will get Shipwreck.
The other option is to offer to just buy the Shipwreck from someone on the boards. Asking price might be somewhat higher than at TLG (unless Travis now has some in stock for the $50 price he has set) but it will surely be less than the price of a full box.