N.Y.I.G., I don't really have an answer for you, but I wanted to pipe up and say I'm in pretty much the same boat. I graduate from a very strong undergraduate program that requires a two year thesis to graduate, got good grades, fulfilled the majority of my language requirements (3 years Czech, 2.5 years of Russian, 1 year intensive German for my historical interests), and want to do a PhD in a similar field as my undergraduate work. I know I'm focused, but I feel like the fact that I'm applying straight out of a BA, even a particularly work-focused one, would make PhD programs nervous or make me seem like a less competitive applicant.
However, the actual constructive part of this post is: the advice I've gotten from my undergraduate advisers is essentially to demonstrate in my application that I have thought long and hard about this despite applying right out of a different program, and to illustrate in my application that I have a concrete idea of what I want to do and how this program fits into goals I first developed as an undergrad.
So good luck! Let me know how it goes.