`read` does not perform macro-expansion: that would break data reading and the reading of quoted forms. macroexpand expands macros at a later stage. Once expanded, macros either refer to primitive special forms or function calls, and it's trivial to determine which. Primitive special forms can have their components macroexpand'd as appropriate. Function calls can be left as-is to be compiled (well, the arguments can be macroexpand'd). Eventually there will just be primitive special forms and raw function calls left, ready to be handed to the compiler.
In idiomatic Lisp code, you either miss lots of the calls, or you have to complicate your code-walker significantly. This is especially the case if you write CL in the (common, but not universal) style that makes significant use of the loop macro, because you either ignore it as a macro, and consider anything inside it opaque until macro-resolution time (because you don't know what it does to its arguments), or you special-case it as a new bit of CL syntax, in which case your parsing is now fancier. Usually you want something like the latter, because source-to-source transformations expect to also replace things inside loops. Same with, say, special-casing setf forms, if you want source-to-source transformations to "do what I mean" in a large number of cases.
It's true that it's very easy to literally get the list representing the code, but there's precious little sensible you can do with that list unless you're willing to descend into some of the more commonly used built-in macros that most CLers treat as de-facto syntax, which requires knowing something about the syntax they in effect define.
For your specific example of replacing calls to foo with another bit of code you may be able to get away with macrolet. (Example: http://letoverlambda.com/index.cl/guest/chap5.html#sec_4 )
A code walker then is mildly complex:
http://www.cs.cmu.edu/afs/cs/project/ai-repository/ai/lang/lisp/code/codewalk/walk/new_walk.cl (read-from-string "#.(print :foo)")