First question: how many is a "large number"? If it's on the order of 10^4 or less, you will probably spend more time fiddling with a script than it would take to do with a more "brute-force" approach. (Given reasonably fast computer, yadda yadda yadda.)

As for the more theoretical question, you would certainly want to use the second approach (with find -exec grep -l foo) to reduce your working file set as much as possible.

Then your next issue is avoiding the overhead of running multiple perls. The -i switch relies on the magic of <>, which is @ARGV if there are command-line arguments, and STDIN if there are not (paraphrasing slightly). However, what you need to do in this case is use both kinds of magic, so your perl will have to be a little more creative. It's harder to do the shuffle that -i does than to read from STDIN manually, so here's one way to try it:

find . -name "*.html" -type f -exec grep -l foo {} \; | perl -pi -e 'B
+EGIN{ @ARGV = <STDIN>; chomp @ARGV };  while (<>) { s/foo/bar/g; } co
+ntinue { print }'
[download]

Notice that you can fiddle with @ARGV before the <> magic takes place. The internals of the script are basically what the -p option does.