Here's a perlish approach as per the way that Mattia Barbon's ExtUtils::FakeConfig achieves the result:
1) Create a Config_m.pm that contains:

package Config_m;
use warnings;
use Config;

my $tied = tied %Config;
$tied->{installsitebin} = '/usr/bin';

1;
[download]

2) Set the PERL5OPT environment variable to -MConfig_m

With the perl5opt environment variable unset, 'perl -V:installsitebin' (and $Config{installsitebin}) still return their original value.
But, when perl5opt is set correctly, 'perl -V:installsitebin' (and $Config{installsitebin}) will return the new value.

Here's a Windows demo (where PERL5OPT is initially unset):

C:\_32\pscrpt>type Config_m.pm
package Config_m;
use warnings;
use Config;

my $tied = tied %Config;
$tied->{installsitebin} = '/usr/bin';

1;

C:\_32\pscrpt>perl -V:installsitebin
installsitebin='c:\MinGW\perl512\bin';

C:\_32\pscrpt>set PERL5OPT=-MConfig_m

C:\_32\pscrpt>perl -V:installsitebin
installsitebin='/usr/bin';

C:\_32\pscrpt>
[download]

One potential annoyance with setting the perl5opt environment variable system-wide is that every perl on the system needs to be able to load a Config_m.pm.

Cheers,
Rob