Well, you could use sed. Or you could use something like the following code.
set tmpname /tmp/something
set source [open $filename]
set destination [open $tmpname w]
set content [read $source]
set lines [split $content \n]
set lines_after_deletion \
[lreplace $lines $line_number_to_remove $line_number_to_remove]
puts -nonewline $destination [join $lines_after_deletion \n]
close $source
close $destination
file rename -force $destination $source
Note, however, that in both of these cases, what you are doing are reading the entire file and writing out the entire file, counting lines.