hmm, somehow the quotes did not survive, I meant:

while read ip;do perl -pi -e "s/^/#/ if /$ip/" script_file; done < ip_
+addr_file
[download]

Also, if you do not want to match 1.2.3.444 with 1.2.3.4, then \b could help:

while read ip;do perl -pi -e "s/^/#/ if /\b$ip\b/" script_file; done <
+ ip_addr_file
[download]

And yes, it modifies the file immediately, and if you run it multiple times, it will keep adding #'s to each line that needs to be REMarked.
In order to NOT do that, I finally propose:

while read ip;do perl -pi -e "s/^#?/#/ if /\b$ip\b/" script_file; done
+ < ip_addr_file
[download]

Drawbacks: It will iterate over the full file for each IP address. There are other solutions proposed, like the one with map, which is more efficient and faster.