$ # Do nothing but count lines
$ time perl -i -pe '++$cnt; END {print STDERR $cnt}' floop.cr
10000000
real    0m2.641s
user    0m2.218s
sys     0m0.375s

$ # Your original filter
$ time perl -i -pe 's/\r//g; ++$cnt; END {print STDERR $cnt}' floop.cr
10000000
real    0m6.298s
user    0m5.703s
sys     0m0.421s

$ # Don't do it globally, end at the first one
$ time perl -i -pe 's/\r//; ++$cnt; END {print STDERR $cnt}' floop.cr
10000000
real    0m3.439s
user    0m2.937s
sys     0m0.390s

$ # Do it only at the end of the line
$ time perl -i -pe 's/\r$//; ++$cnt; END {print STDERR $cnt}' floop.cr
10000000
real    0m3.188s
user    0m2.781s
sys     0m0.359s