Yes, you're correct. Automator is a vehicle without steering. I would avoid automator in the first place rather than wasting time in clearing up its mess...
As for the useless output from /usr/bin/automator, you can neither use it as input to next shell command nor next automator action without clearing those stupid parentheses, quotes, commas and indent spaces.
Here're some options:
1) Provided that the external automator workflow you're invoking by /usr/bin/automator via "do shell script" command consists of a Run Shell Script action, invoke the shell script in the action directly by "do shell script" command in AppleScript. In other words, write everything in AppleScript or shell script without resorting to some poor Automator facility.
E.g., Given that shell script in a Run Shell Script action is as follows:
#!/bin/bash
for f in "$@"
do
echo "$f"
done
and a workflow ~/Desktop/a.workflow consisting of the single action is invoked by /usr/bin/automator as follows:
do shell script "/usr/bin/automator -i 'file 1
file 2
file 3' ~/Desktop/a.workflow"
then replace it with the following:
do shell script "/bin/bash -s <<'EOF' - 'file 1' 'file 2' 'file 3'
for f in \"$@\"
do
echo \"$f\"
done
EOF"
which will return:
file 1
file 2
file 3
and you may convert it into AppleScript list by getting the pargraphs of it.
2) Bother yourself to clear up the output's mess of /usr/bin/automator.
E.g., Given the same assumptions in 1), use this:
do shell script "/usr/bin/automator -i 'file 1
file 2
file 3' ~/Desktop/a.workflow | sed -En 's/\"?,?$//; s/[[:space:]]+\"?(.*)$/\\1/p'"
which will return:
file 1
file 2
file 3
* Note that the sed(1) code in 2) only works with workflow with Run Shell Script action because Run AppleScript action yields output in different format when run by /usr/bin/automator. Also in 2), you cannot handle filename containing linefeed character due to the limitation of /usr/bin/automator whereas you can handle it in 1) by adapting shell script and AppleScript so as to use \0 for output line separator.
Observed and tested under OS X 10.6.8. Later versions may possibly vary.
Good luck,
H