Just to let you know that you are not alone!

Installed pandoc today and it runs fine for tex, html and word documents. 
pdf documents throw the exact same error you are seeing.

> pandoc --filter pandoc-citeproc SCG.protocol.md -s -o SCG.pdf
pandoc: pdflatex: createProcess: runInteractiveProcess: exec: inappropriate 
type (Not a directory)

>which pdflatex
/usr/texbin/pdflatex

>pdflatex -v
pdfTeX 3.14159265-2.6-1.40.15 (TeX Live 2014)
kpathsea version 6.2.0
Copyright 2014 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
There is NO warranty.  Redistribution of this software is
covered by the terms of both the pdfTeX copyright and
the Lesser GNU General Public License.
For more information about these matters, see the file
named COPYING and the pdfTeX source.
Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
Compiled with libpng 1.6.10; using libpng 1.6.10
Compiled with zlib 1.2.8; using zlib 1.2.8

>pandoc -v
pandoc 1.13.1
Compiled with texmath 0.8, highlighting-kate 0.5.11.
Syntax highlighting is supported for the following languages:
    abc, actionscript, ada, agda, apache, asn1, asp, awk, bash, bibtex, 
boo, c,
    changelog, clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css,
    curry, d, diff, djangotemplate, dockerfile, dot, doxygen, doxygenlua, 
dtd,
    eiffel, email, erlang, fasm, fortran, fsharp, gcc, glsl, gnuassembler, 
go,
    haskell, haxe, html, ini, isocpp, java, javadoc, javascript, json, jsp,
    julia, latex, lex, lilypond, literatecurry, literatehaskell, lua, m4,
    makefile, mandoc, markdown, mathematica, matlab, maxima, mediawiki,
    metafont, mips, modelines, modula2, modula3, monobasic, nasm, noweb,
    objectivec, objectivecpp, ocaml, octave, opencl, pascal, perl, php, 
pike,
    postscript, prolog, pure, python, r, relaxng, relaxngcompact, rest, 
rhtml,
    roff, ruby, rust, scala, scheme, sci, sed, sgml, sql, sqlmysql,
    sqlpostgresql, tcl, tcsh, texinfo, verilog, vhdl, xml, xorg, xslt, xul,
    yacc, yaml, zsh


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