Sorry, you're right, I misread your post. I think you have a good point here, but to be fair I don't think people weren't thinking in evolutionary terms at all. Not everything in our (or other animals') bodies are actually there for a good reason now. I'll give you one good example: horse toes. I don't remember the exact term now, but horses equine ancestors used to have multiple toes, like us and many other mammals. Now they just have one, with a big fingernail, called a "hoof". But if you look closely at the anatomy of their legs, you'll see some of the vestigial toes still there, serving no useful purpose now. Evolution isn't like engineering design, where we improve a design, see something that's not needed any more (like an automotive engine distributor), and just remove it entirely, and everything related to that, in one clean sweep, even mundane small things like bolt holes, and optimize the design for the new system (being coil-on-plug for this analogy). With evolution, it's slow and gradual. Another example is the recurrent sublaryngeal nerve in humans: this nerve apparently takes a rather bewildering and inefficient route, for seemingly no good reason, but when looked at from an evolutionary perspective, it makes sense why it takes that route. (The nerve itself is not vestigial and serves an important purpose, but the route it takes is very sub-optimal and could be called "vestigial" in a way.)

[1] http://www.thehorse.com/articles/34382/where-did-horses-extr...

[2] https://unzipyourgenes.wordpress.com/2011/03/24/unintelligen...

So I think it's entirely reasonable, in the absence of contradictory evidence, to use evolutionary thinking to make an argument that an anatomical structure seems to serve no purpose any more, just like those extra horse toes. Unfortunately, they were obviously wrong about the appendix, and I do think it's a little dangerous because the assumption of vestigiality rests upon the lack of evidence for the part having a modern use, but this can cause people to stop looking for that modern use, and then we wind up with what happened to the appendix, where it took a really long time to learn the truth because we assumed we already knew.