I simply kill the process upon exit. That's not the most grateful thing but it works:

package App::VideoMixer::External::FFmpeg;
use strict;

use vars qw($VERSION);
$VERSION = '0.02';

use parent 'Class::Accessor';
__PACKAGE__->mk_accessors(qw(width height depth pid stream texture_id 
+file pixel_format ffmpeg));

sub spawn {
    my ($self,$cmd) = @_;
    my $pid = open my $stream, $cmd
        or die "Couldn't spawn '$cmd': $!/$?";
    binmode $stream;
    return ($pid,$stream)
};

sub DESTROY {
    if (my $pid = $_[0]->pid) {
        kill 9, $pid
    };
};
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This will kill the external process once the object gets destroyed. You can read the data from $stream and you have to set $self->pid to the returned $pid (and looking at this code, I'm not sure why ->spawn does it that way instead of setting $pid instead - I guess it's because I turned a subroutine into an object later).

As a side note, App::VideoMixer v0.02 is in a sad state, as even the distribution is incomplete, so I'll have to release a fixed version soonish.