There is a huge difference between "terrible" and "not ideal for every situation." In the case you just presented, the only disadvantage over the old system is that instead of the new player having a red thumb (or possibly several, depending on how many other players were at the table), they simply have a disconnect ratio of 100%. Considering that a disconnect ratio of over 10% is a warning to most players....
Also, remember this applies to
one game per account. When presented with any new situation, most people are bound to make decisions that are not what people familiar with the situation would make. These decisions may offend. Newbie protection gives people a chance to make a mistake, and learn from it, without being haunted by it for a long time.
There are other gaming sites that I avoid because there is no grace like this. One example that is coming to mind is someone created an account and joined an open table. They were immediately criticized in chat for not waiting for an invitation, which apparently was the undocumented norm on that site. BGA may have norms which seem weird to people new to the site. We should give them a chance to learn.
Edit --
Of course, there is a way to avoid this. Never join a table where a new player exists. Always kick new players from one's table if one is the administrator. Always refuse to start a game if a new player joins later, and request the administrator kick either oneself or the new player off. One will then never have to deal with not being able to squash someone under their red thumb, and no changes need to be made to the reputation system -- just in how one uses it.