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With sed and a loop
sed '
:L
s/\([0-9]\{1,\}\),/ \1/
tL
' file

Hi.

Using the free utility align:
#!/usr/bin/env bash

# @(#) s1 Demonstrate automatic field alignment, align.

# Utility functions: print-as-echo, print-line-with-visual-space, debug....

Small correction:
awk '
BEGIN {
FS="!"; OFS="!"
}
{
for (i=1;i<=NF;i++) {
l=length($i)
gsub(/,/,x,$i)
$i=sprintf("%*s",l,$i)
}
print
}
' file
...

sed might not be the tool of choice, then. Use either of the awk proposals and loop across the columns in question.

A different approach that should also work if there is more than one thousands separator:
awk '{$4=sprintf("%*s",gsub(/,/,x,$4),x)$4}1' FS=! OFS=! file

--
x represents an empty string here. The...

awk -F! '{if(sub(",", "", $4)){$4=" "$4}}1' OFS=! adam1969in.file

sed 's/\([0-9]*\),/ \1/' adam1969in.file
perl -pe 's/(\d+),/ $1/' adam1969in.file