OK, I'll try to be more precise this time, so I hope that you reconsider at least a few things:

First, I think that the main misunderstanding is, as you mentioned, your somewhat incomplete experience of Clojure.

Second, perhaps there is a tiny bit of a strawman fallacy in your argument. Why? Well, def is not for defining "variables". It does get mentioned many times in Clojure literature: these are vars, you can change them, but they are NOT there for the regular data, but to enable you to give names to your functions and the rest of clojure artefacts. The programmer does not need to use metaprogramming or macros to shoot himself in the foot using vars as "variables". How does that relate to the wikipedia definition of referential transparency? Well, only PURE functions are referentially transparent. Def is not pure, and it is not even a function - it is a special form. Of course, it could be confusing for a novice, but it has been clearly stated many times in the literature how and why, so to anyone ho has learned the basics well and is not trying to recreate Java/python/Ruby/C coding style in Clojure, that should not be a source of problems.

As for your macro example, the first part of your argument, "First, I'll show that the argument that it takes must be the code itself, rather than the result of evaluating the code" - that is something macros are for, so the programmer expects exactly what you described, although you did not need a macro for swapping arguments in a function call.

I hope that we agree that, if we know that there are two phases in Cloure compilation process, a "macro" phase and a "regular code" phase, then everything is fine and clear. I understand that your complaint is that the programmer might forget that so she might be confused in the examples that you stated, so I will continue with that assumption in mind.

Let's try referential transparency with the function foo:

1) Is the function foo referentially transparent?

user=> (defn foo [a b] (swapargs (mod a b)))
#'user/foo

user=> (foo 7 5)

5

user=> (foo 10 8)

8

user=> (foo 10 8)

8

user=> (foo 10 8)

8

user=> (foo 7 5)

5

As we can see, "the same function (foo) with the same arguments will always produce the same result, and that you can call it more (throwing away the result) or fewer (replacing calls with the result) times without affecting the meaning of the program".

2) Is swapargs macro referentially transparent?

user=> (swapargs (mod 7 5))

5

user=> (swapargs (mod 7 5))

5

user=> (swapargs (mod 7 5))

5

user=> (swapargs (mod 10 8))

8

user=> (swapargs (mod 10 8))

8

Is "the same function (swapargs) with the same arguments will always produce the same result, and that you can call it more (throwing away the result) or fewer (replacing calls with the result) times without affecting the meaning of the program"?
Well, is swapargs a function? -No, but let's forget that for a sake of being fair. The proper way to resolve this is to read the documentation of swapargs. And the documentation would say that the argument to swapargs is a clojure form (something like (mod 7 5)), not a number (something like the result of calling (mod 7 5)). If we having that in mind, it is clear that swapargs is also referentially transparent, with regards to its argumens. We CAN replace swapargs with its result, s you can see in the aforementioned code. If we want our argument so be the results of (mod 7 5) we would use a function, not a macro!

With the rest of your post, I agree. Macros are not superpowerful, you can shoot yourself in the foot with them (and every lisp book warns you about that in many ways), and haskell is awasome in many ways.
There could be many pitfals with clojure and macros, but I think these pitfalls are not of the kind that your examples show :)