Unlikely that it will kill off the Marketplace.
I understand your concerns, but I do not share them, at the very least not to the same extent. The Marketplace will still be well-used because
(i) People have existing characters they want to upgrade/BiS-out, giving them no other option than to use the Marketplace
(ii) BiS items on the Marketplace are 23 Coins a pop (Ragnaros/Deathwing), which is quite affordable. Characters on the trading for 50 Coins will likely not have any BiS items at all, which would make them cheap, entry-level characters. Buyers of those might still use the Marketplace eventually (see (i).
(iii) BiS characters are quite rare, and worth quite a bit. It is quite possible that there will be an initial 'run' at the trading, but eventually I would assume that they will settle at a decent price (around 200 to 300 Coins, which is not too far away from the Marketplace ballpark). The influx of many BiS items are also mostly regulated through the Marketplace because there are only a small handful of people who can acquire them through drops.
(iv) People have different opinions and preferences on what is considered 'BiS' or not; very unlikely that the trading will be able to offer something, if anything at all that suits everyone. Those people will still resort to the Marketplace.
(v) It`s far more common for people to drop $30 on an item every now and then than $300 at once for a character from the trading, which again, will direct them to the Marketplace.